Recombinant milk proteins

ABSTRACT

Provided herein are compositions and methods for producing recombinant milk proteins, as well as food compositions comprising the same. In aspects, the recombinant milk proteins of the disclosure are recombinant fusion proteins comprising casein and beta-lactoglobulin.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/326,785 (now U.S. Pat. No. 11,142,555), filed May 21, 2021, which isa continuation of U.S. patent application Ser. No. 17/127,090 (now U.S.Pat. No. 11,034,743), filed Dec. 18, 2020, which is a continuation ofSer. No. 17/039,760 (now. U.S. Pat. No. 10,894,812), filed Sep. 30,2020, the disclosures of which are hereby incorporated by reference intheir entirety.

DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY

The contents of the text file submitted electronically herewith areincorporated herein by reference in their entirety: A computer readableformat copy of the Sequence Listing filename:ALRO_007_14US_SeqList_ST25.txt, date recorded: Oct. 4, 2021, file size155 kilobytes.

FIELD OF THE DISCLOSURE

The present disclosure generally relates to recombinant milk proteins.The disclosure also relates to food compositions comprising recombinantmilk proteins.

BACKGROUND

Globally, more than 7.5 billion people around the world consume milk andmilk products. Demand for cow milk and dairy products is expected tokeep increasing due to increased reliance on these products indeveloping countries as well as growth in the human population, which isexpected to exceed 9 billion people by 2050.

Relying on animal agriculture to meet the growing demand for food is nota sustainable solution. According to the Food & Agriculture Organizationof the United Nations, animal agriculture is responsible for 18% of allgreenhouse gases, more than the entire transportation sector combined.Dairy cows alone account for 3% of this total.

In addition to impacting the environment, animal agriculture poses aserious risk to human health. A startling 80% of antibiotics used in theUnited States go towards treating animals, resulting in the developmentof antibiotic resistant microorganisms also known as superbugs. Foryears, food companies and farmers have administered antibiotics not onlyto sick animals, but also to healthy animals, to prevent illness. InSeptember 2016, the United Nations announced the use of antibiotics inthe food system as a crisis on par with Ebola and HIV.

It is estimated that cow milk accounts for 83% of global milkproduction. Accordingly, there is an urgent need for to provide bovinemilk and/or essential high-quality proteins from bovine milk in a moresustainable and humane manner, instead of solely relying on animalfarming. Also, there is a need for selectively producing the specificmilk proteins that confer nutritional and clinical benefits, and/or donot provoke allergic responses.

BRIEF SUMMARY

Provided herein are compositions and methods for producing milk proteinsin transgenic plants. In some embodiments, a milk protein is stablyexpressed in a transgenic plant by fusing it to a stable protein, suchas a stable mammalian, avian, plant or fungal protein. The compositionsand methods provided herein allow for safe, sustainable and humaneproduction of milk proteins for commercial use, such as use in foodcompositions.

In some embodiments, the disclosure provides a stably transformed plantcomprising in its genome: a recombinant DNA construct encoding a fusionprotein, the fusion protein comprising: (i) an unstructured milkprotein, and (ii) a structured animal protein; wherein the fusionprotein is stably expressed in the plant in an amount of 1% or higherper total protein weight of soluble protein extractable from the plant.

In some embodiments, the disclosure provides a stably transformed plant,comprising in its genome: a recombinant DNA construct encoding a fusionprotein, the fusion protein comprising: κ-casein; and β-lactoglobulin;wherein the fusion protein is stably expressed in the plant in an amountof 1% or higher per total protein weight of soluble protein extractablefrom the plant.

In some embodiments, the disclosure provides a recombinant fusionprotein comprising: (i) an unstructured milk protein, and (ii) astructured animal protein.

In some embodiments, the disclosure provides a plant-expressedrecombinant fusion protein, comprising: κ-casein and β-lactoglobulin.

Also provided are nucleic acids encoding the recombinant fusion proteinsdescribed herein.

Also provided are vectors comprising a nucleic acid encoding one or morerecombinant fusion proteins described herein, wherein the recombinantfusion protein comprises: (i) an unstructured milk protein, and (ii) astructured animal protein.

Also provided are plants comprising the recombinant fusion proteinsand/or the nucleic acids described herein.

The instant disclosure also provides a method for stably expressing arecombinant fusion protein in a plant, the method comprising: a)transforming a plant with a plant transformation vector comprising anexpression cassette comprising: a sequence encoding a fusion protein,wherein the fusion protein comprises an unstructured milk protein, and astructured animal protein; and b) growing the transformed plant underconditions wherein the recombinant fusion protein is expressed in anamount of 1% or higher per total protein weight of soluble proteinextractable from the plant.

Also provided herein are methods for making food compositions, themethods comprising: expressing the recombinant fusion protein in aplant; extracting the recombinant fusion protein from the plant;optionally, separating the milk protein from the structured animalprotein or the structured plant protein; and creating a food compositionusing the milk protein or the fusion protein.

Also provided herein are food compositions comprising one or morerecombinant fusion proteins as described herein.

Also provided are food compositions produced using any one of themethods disclosed herein.

These and other embodiments are described in detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying figures, which are incorporated herein and form a partof the specification, illustrate some, but not the only or exclusive,example embodiments and/or features. It is intended that the embodimentsand figures disclosed herein are to be considered illustrative ratherthan limiting.

FIGS. 1A, 1B, 1C, 1D, 1E, IF, 1G, 1H, 1I, 1J, 1K, 1L, 1M, 1N, 1O, and 1Pshow expression cassettes having different combinations of fusionsbetween structured and intrinsically unstructured proteins (not toscale). Coding regions and regulatory sequences are indicated as blocks(not to scale). As used in the figures, “L” refers to linker; “Sig”refers to a signal sequence that directs foreign proteins to proteinstorage vacuoles, “5′ UTR” refers to the 5′ untranslated region, and“KDEL” refers to an endoplasmic reticulum retention signal.

FIG. 2 shows the modified pAR15-00 cloning vector containing aselectable marker cassette conferring herbicide resistance. Codingregions and regulatory sequences are indicated as blocks (not to scale).

FIG. 3 shows an example expression cassette comprising a OKC1-T:OLG1(Optimized Kappa Casein version 1:beta-lactoglobulin version 1, SEQ IDNOs: 71-72) fusion driven by PvPhas promoter fused with arc5′UTR:sig10,followed by the ER retention signal (KDEL) and the 3′UTR of the arc5-1gene, “arc-terminator”. “arc5′UTR” refers to the 5′ untranslated regionof the arc5-1 gene. “Sig10” refers to the lectin 1 gene signal peptide.“RB” refers to ribosomal binding site. Coding regions and regulatorysequences are indicated as blocks (not to scale).

FIG. 4 shows an example expression cassette comprising a OBC-T2:FM:OLG1(Optimized Beta Casein Truncated version 2:Chymosin cleavagesite:beta-lactoglobulin version 1, SEQ ID NOs: 73-74) fusion driven byPvPhas promoter fused with arc5′UTR:sig10, followed by the 3′UTR of thearc5-1 gene, “arc-terminator”. “arc5′UTR” refers to the 5′ untranslatedregion of the arc5-1 gene. “Sig10” refers to the lectin 1 gene signalpeptide. “RB” refers to ribosomal binding site. Coding regions andregulatory sequences are indicated as blocks (not to scale). The BetaCasein is “truncated” in that the bovine secretion signal is removed,and replaced with a plant targeting signal.

FIG. 5 shows an example expression cassette comprising a OaS1-T:FM:OLG1(Optimized Alpha S1 Casein Truncated version 1:Chymosin cleavagesite:beta-lactoglobulin version 1, SEQ ID NOs: 75-76) fusion driven byPvPhas promoter fused with arc5′UTR:sig10, followed by the 3′UTR of thearc5-1 gene, “arc-terminator”. “arc5′UTR” refers to the 5′ untranslatedregion of the arc5-1 gene. “Sig10” refers to the lectin 1 gene signalpeptide. “RB” refers to ribosomal binding site. Coding regions andregulatory sequences are indicated as blocks (not to scale). The AlphaS1 Casein is “truncated” in that the bovine secretion signal is removed,and replaced with a plant targeting signal.

FIG. 6 shows an example expression cassette comprising apara-OKC1-T:FM:OLG1:KDEL (Optimized paraKappa Casein version 1:Chymosincleavage site:beta-lactoglobulin version 1, SEQ ID NOs: 77-78) fusiondriven by PvPhas promoter fused with arc5′UTR:sig 10, followed by the ERretention signal (KDEL) and the 3′UTR of the arc5-1 gene,“arc-terminator”. “arc5′UTR” refers to the 5′ untranslated region of thearc5-1 gene. “Sig10” refers to the lectin 1 gene signal peptide. “RB”refers to ribosomal binding site. Coding regions and regulatorysequences are indicated as blocks (not to scale).

FIG. 7 shows an example expression cassette comprising apara-OKC1-T:FM:OLG1 (Optimized paraKappa Casein version 1:Chymosincleavage site:beta-lactoglobulin version 1, SEQ ID NOs: 79-80) fusiondriven by PvPhas promoter fused with arc5′UTR:sig 10, followed by the3′UTR of the arc5-1 gene, “arc-terminator.” “arc5′UTR” refers to the 5′untranslated region of the arc5-1 gene. “Sig10” refers to the lectin 1gene signal peptide. “RB” refers to ribosomal binding site. Codingregions and regulatory sequences are indicated as blocks (not to scale).

FIG. 8 shows an example expression cassette comprising a OKC1-T:OLG1(Optimized Kappa Casein version 1:beta-lactoglobulin version 1, SEQ IDNOs: 81-82) fusion that is driven by the promoter and signal peptide ofglycinin 1 (GmSeed2:sig2) followed by the ER retention signal (KDEL) andthe nopaline synthase gene termination sequence, (nos term). Codingregions and regulatory sequences are indicated as blocks (not to scale).

FIGS. 9A, 9B, 9C, and 9D show protein detection by western blotting.FIG. 9A shows detection of the fusion protein using a primary antibodyraised against κ-casein (kCN). The kCN commercial protein is detected atan apparent MW of ˜26 kDa (theoretical: 19 kDa—arrow). The fusionprotein is detected at an apparent MW of ˜40 kDa (theoretical: 38kDa—arrowhead). FIG. 9B shows detection of the fusion protein using aprimary antibody raised against β-lactoglobulin (LG). The LG commercialprotein is detected at an apparent MW of ˜18 kDa (theoretical: 18kDa—arrow). The fusion protein is detected at an apparent MW of ˜40 kDa(theoretical: 38 kDa—arrowhead). FIGS. 9C and 9D show protein gels ascontrol for equal lane loading (image is taken at the end of the SDSrun).

FIGS. 10A and 10B show two illustrative fusion proteins. In FIG. 10A, aκ-casein protein is fused to a β-lactoglobulin protein. The κ-caseincomprises a natural chymosin cleavage site (arrow 1). Cleavage of thefusion protein with rennet (or chymosin) yields two fragments: apara-kappa casein fragment, and a fragment comprising a κ-caseinmacropeptide fused to β-lactoglobulin. In some embodiments, a secondprotease cleavage site may be added at the C-terminus of the k-caseinprotein (i.e., at arrow 2), in order to further allow separation of theκ-casein macropeptide and the β-lactoglobulin. The second proteasecleavage site may be a rennet cleavage site (e.g., a chymosin cleavagesite), or it may be a cleavage site for a different protease. In FIG.10B, a para-κ-casein protein is fused directly to β-lactoglobulin. Aprotease cleavage site (e.g., a rennet cleavage site) is added betweenthe para-κ-casein and the β-lactoglobulin to allow for separationthereof. By fusing the para-κ-casein directly to the β-lactoglobulin, noκ-casein macropeptide is produced.

FIG. 11 is a flow-chart showing an illustrative process for producing afood composition comprising an unstructured milk protein, as describedherein.

DETAILED DESCRIPTION

The following description includes information that may be useful inunderstanding the present disclosure. It is not an admission that any ofthe information provided herein is prior art or relevant to thepresently claimed disclosures, or that any publication specifically orimplicitly referenced is prior art.

Definitions

While the following terms are believed to be well understood by one ofordinary skill in the art, the following definitions are set forth tofacilitate explanation of the presently disclosed subject matter.

All technical and scientific terms used herein, unless otherwise definedbelow, are intended to have the same meaning as commonly understood byone of ordinary skill in the art. References to techniques employedherein are intended to refer to the techniques as commonly understood inthe art, including variations on those techniques and/or substitutionsof equivalent techniques that would be apparent to one of skill in theart.

As used herein, the singular forms “a,” “an,” and “the” include pluralreferents unless the content clearly dictates otherwise.

The term “about” or “approximately” when immediately preceding anumerical value means a range (e.g., plus or minus 10% of that value).For example, “about 50” can mean 45 to 55, “about 25,000” can mean22,500 to 27,500, etc., unless the context of the disclosure indicatesotherwise, or is inconsistent with such an interpretation. For example,in a list of numerical values such as “about 49, about 50, about 55, . .. ”, “about 50” means a range extending to less than half theinterval(s) between the preceding and subsequent values, e.g., more than49.5 to less than 52.5. Furthermore, the phrases “less than about” avalue or “greater than about” a value should be understood in view ofthe definition of the term “about” provided herein. Similarly, the term“about” when preceding a series of numerical values or a range of values(e.g., “about 10, 20, 30” or “about 10-30”) refers, respectively to allvalues in the series, or the endpoints of the range.

As used herein, “mammalian milk” can refer to milk derived from anymammal, such as bovine, human, goat, sheep, camel, buffalo, waterbuffalo, dromedary, llama and any combination thereof. In someembodiments, a mammalian milk is a bovine milk.

As used herein, “structured” refers to those proteins having awell-defined secondary and tertiary structure, and “unstructured” refersto proteins that do not have well defined secondary and/or tertiarystructures. An unstructured protein may also be described as lacking afixed or ordered three-dimensional structure. “Disordered” and“intrinsically disordered” are synonymous with unstructured.

As used herein, “rennet” refers to a set of enzymes typically producedin the stomachs of ruminant mammals. Chymosin, its key component, is aprotease enzyme that cleaves κ-casein (to produce para-κ-casein). Inaddition to chymosin, rennet contains other enzymes, such as pepsin andlipase. Rennet is used to separate milk into solid curds (forcheesemaking) and liquid whey. Rennet or rennet substitutes are used inthe production of most cheeses.

As used herein “whey” refers to the liquid remaining after milk has beencurdled and strained, for example during cheesemaking. Whey comprises acollection of globular proteins, typically a mixture of β-lactoglobulin,α-lactalbumin, bovine serum albumin, and immunoglobulins.

The term “plant” includes reference to whole plants, plant organs, planttissues, and plant cells and progeny of same, but is not limited toangiosperms and gymnosperms such as Arabidopsis, potato, tomato,tobacco, alfalfa, lettuce, carrot, strawberry, sugarbeet, cassava, sweetpotato, soybean, lima bean, pea, chick pea, maize (corn), turf grass,wheat, rice, barley, sorghum, oat, oak, eucalyptus, walnut, palm andduckweed as well as fern and moss. Thus, a plant may be a monocot, adicot, a vascular plant reproduced from spores such as fern or anonvascular plant such as moss, liverwort, hornwort and algae. The word“plant,” as used herein, also encompasses plant cells, seeds, plantprogeny, propagule whether generated sexually or asexually, anddescendants of any of these, such as cuttings or seed. Plant cellsinclude suspension cultures, callus, embryos, meristematic regions,callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen,seeds and microspores. Plants may be at various stages of maturity andmay be grown in liquid or solid culture, or in soil or suitable media inpots, greenhouses or fields. Expression of an introduced leader, traileror gene sequences in plants may be transient or permanent.

The term “vascular plant” refers to a large group of plants that aredefined as those land plants that have lignified tissues (the xylem) forconducting water and minerals throughout the plant and a specializednon-lignified tissue (the phloem) to conduct products of photosynthesis.Vascular plants include the clubmosses, horsetails, ferns, gymnosperms(including conifers) and angiosperms (flowering plants). Scientificnames for the group include Tracheophyta and Tracheobionta. Vascularplants are distinguished by two primary characteristics. First, vascularplants have vascular tissues which distribute resources through theplant. This feature allows vascular plants to evolve to a larger sizethan non-vascular plants, which lack these specialized conductingtissues and are therefore restricted to relatively small sizes. Second,in vascular plants, the principal generation phase is the sporophyte,which is usually diploid with two sets of chromosomes per cell. Only thegerm cells and gametophytes are haploid. By contrast, the principalgeneration phase in non-vascular plants is the gametophyte, which ishaploid with one set of chromosomes per cell. In these plants, only thespore stalk and capsule are diploid.

The term “non-vascular plant” refers to a plant without a vascularsystem consisting of xylem and phloem. Many non-vascular plants havesimpler tissues that are specialized for internal transport of water.For example, mosses and leafy liverworts have structures that look likeleaves, but are not true leaves because they are single sheets of cellswith no stomata, no internal air spaces and have no xylem or phloem.Non-vascular plants include two distantly related groups. The firstgroup are the bryophytes, which is further categorized as three separateland plant Divisions, namely Bryophyta (mosses), Marchantiophyta(liverworts), and Anthocerotophyta (hornworts). In all bryophytes, theprimary plants are the haploid gametophytes, with the only diploidportion being the attached sporophyte, consisting of a stalk andsporangium. Because these plants lack lignified water-conductingtissues, they can't become as tall as most vascular plants. The secondgroup is the algae, especially the green algae, which consists ofseveral unrelated groups. Only those groups of algae included in theViridiplantae are still considered relatives of land plants.

The term “plant part” refers to any part of a plant including but notlimited to the embryo, shoot, root, stem, seed, stipule, leaf, petal,flower bud, flower, ovule, bract, trichome, branch, petiole, internode,bark, pubescence, tiller, rhizome, frond, blade, ovule, pollen, stamen,and the like. The two main parts of plants grown in some sort of media,such as soil or vermiculite, are often referred to as the “above-ground”part, also often referred to as the “shoots”, and the “below-ground”part, also often referred to as the “roots”.

The term “plant tissue” refers to any part of a plant, such as a plantorgan. Examples of plant organs include, but are not limited to theleaf, stem, root, tuber, seed, branch, pubescence, nodule, leaf axil,flower, pollen, stamen, pistil, petal, peduncle, stalk, stigma, style,bract, fruit, trunk, carpel, sepal, anther, ovule, pedicel, needle,cone, rhizome, stolon, shoot, pericarp, endosperm, placenta, berry,stamen, and leaf sheath.

The term “seed” is meant to encompass the whole seed and/or all seedcomponents, including, for example, the coleoptile and leaves, radicleand coleorhiza, scutellum, starchy endosperm, aleurone layer, pericarpand/or testa, either during seed maturation and seed germination.

The term “transgenic plant” means a plant that has been transformed withone or more exogenous nucleic acids. “Transformation” refers to aprocess by which a nucleic acid is stably integrated into the genome ofa plant cell. “Stably integrated” refers to the permanent, ornon-transient retention and/or expression of a polynucleotide in and bya cell genome. Thus, a stably integrated polynucleotide is one that is afixture within a transformed cell genome and can be replicated andpropagated through successive progeny of the cell or resultanttransformed plant. Transformation may occur under natural or artificialconditions using various methods well known in the art. Transformationmay rely on any known method for the insertion of nucleic acid sequencesinto a prokaryotic or eukaryotic host cell, includingAgrobacterium-mediated transformation protocols, viral infection,whiskers, electroporation, heat shock, lipofection, polyethylene glycoltreatment, micro-injection, and particle bombardment.

As used herein, the terms “stably expressed” or “stable expression”refer to expression and accumulation of a protein in a plant cell overtime. In some embodiments, a protein may accumulate because it is notdegraded by endogenous plant proteases. In some embodiments, a proteinis considered to be stably expressed in a plant if it is present in theplant in an amount of 1% or higher per total protein weight of solubleprotein extractable from the plant.

As used herein, the term “fusion protein” refers to a protein comprisingat least two constituent proteins (or fragments or variants thereof)that are encoded by separate genes, and that have been joined so thatthey are transcribed and translated as a single polypeptide. In someembodiments, a fusion protein may be separated into its constituentproteins, for example by cleavage with a protease.

The term “recombinant” refers to nucleic acids or proteins formed bylaboratory methods of genetic recombination (e.g., molecular cloning) tobring together genetic material from multiple sources, creatingsequences that would not otherwise be found in the genome. A recombinantfusion protein is a protein created by combining sequences encoding twoor more constituent proteins, such that they are expressed as a singlepolypeptide. Recombinant fusion proteins may be expressed in vivo invarious types of host cells, including plant cells, bacterial cells,fungal cells, mammalian cells, etc. Recombinant fusion proteins may alsobe generated in vitro.

The term “promoter” or a “transcription regulatory region” refers tonucleic acid sequences that influence and/or promote initiation oftranscription. Promoters are typically considered to include regulatoryregions, such as enhancer or inducer elements. The promoter willgenerally be appropriate to the host cell in which the target gene isbeing expressed. The promoter, together with other transcriptional andtranslational regulatory nucleic acid sequences (also termed “controlsequences”), is necessary to express any given gene. In general, thetranscriptional and translational regulatory sequences include, but arenot limited to, promoter sequences, ribosomal binding sites,transcriptional start and stop sequences, translational start and stopsequences, and enhancer or activator sequences.

The term signal peptide—also known as “signal sequence”, “targetingsignal”, “localization signal”, “localization sequence”, “transitpeptide”, “leader sequence”, or “leader peptide”, is used herein torefer to an N-terminal peptide which directs a newly synthesized proteinto a specific cellular location or pathway. Signal peptides are oftencleaved from a protein during translation or transport, and aretherefore not typically present in a mature protein.

The term “proteolysis” or “proteolytic” or “proteolyze” means thebreakdown of proteins into smaller polypeptides or amino acids.Uncatalyzed hydrolysis of peptide bonds is extremely slow. Proteolysisis typically catalyzed by cellular enzymes called proteases, but mayalso occur by intra-molecular digestion. Low pH or high temperatures canalso cause proteolysis non-enzymatically. Limited proteolysis of apolypeptide during or after translation in protein synthesis oftenoccurs for many proteins. This may involve removal of the N-terminalmethionine, signal peptide, and/or the conversion of an inactive ornon-functional protein to an active one.

The term “2A peptide”, used herein, refers to nucleic acid sequenceencoding a 2A peptide or the 2A peptide itself. The average length of 2Apeptides is 18-22 amino acids. The designation “2A” refers to a specificregion of picornavirus polyproteins and arose from a systematicnomenclature adopted by researchers. In foot-and-mouth disease virus(FMDV), a member of Picornaviridae family, a 2A sequence appears to havethe unique capability to mediate cleavage at its own C-terminus by anapparently enzyme-independent, novel type of reaction. This sequence canalso mediate cleavage in a heterologous protein context in a range ofeukaryotic expression systems. The 2A sequence is inserted between twogenes of interest, maintaining a single open reading frame. Efficientcleavage of the polyprotein can lead to co-ordinate expression of activetwo proteins of interest. Self-processing polyproteins using the FMDV 2Asequence could therefore provide a system for ensuring coordinated,stable expression of multiple introduced proteins in cells includingplant cells.

The term “purifying” is used interchangeably with the term “isolating”and generally refers to the separation of a particular component fromother components of the environment in which it was found or produced.For example, purifying a recombinant protein from plant cells in whichit was produced typically means subjecting transgenic protein containingplant material to biochemical purification and/or column chromatography.

When referring to expression of a protein in a specific amount per thetotal protein weight of the soluble protein extractable from the plant(“TSP”), it is meant an amount of a protein of interest relative to thetotal amount of protein that may reasonably be extracted from a plantusing standard methods. Methods for extracting total protein from aplant are known in the art. For example, total protein may be extractedfrom seeds by bead beating seeds at about 15000 rpm for about 1 min. Theresulting powder may then be resuspended in an appropriate buffer (e.g.,50 mM Carbonate-Bicarbonate pH 10.8, 1 mM DTT, 1× Protease InhibitorCocktail). After the resuspended powder is incubated at about 4° C. forabout 15 minutes, the supernatant may be collected after centrifuging(e.g., at 4000 g, 20 min, 4° C.). Total protein may be measured usingstandard assays, such as a Bradford assay. The amount of protein ofinterest may be measured using methods known in the art, such as anELISA or a Western Blot.

When referring to a nucleic acid sequence or protein sequence, the term“identity” is used to denote similarity between two sequences. Sequencesimilarity or identity may be determined using standard techniques knownin the art, including, but not limited to, the local sequence identityalgorithm of Smith & Waterman, Adv. Appl. Math. 2, 482 (1981), by thesequence identity alignment algorithm of Needleman & Wunsch, J Mol.Biol. 48,443 (1970), by the search for similarity method of Pearson &Lipman, Proc. Natl. Acad. Sci. USA 85, 2444 (1988), by computerizedimplementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe Wisconsin Genetics Software Package, Genetics Computer Group, 575Science Drive, Madison, Wis.), the Best Fit sequence program describedby Devereux et al., Nucl. Acid Res. 12, 387-395 (1984), or byinspection. Another suitable algorithm is the BLAST algorithm, describedin Altschul et al., J Mol. Biol. 215, 403-410, (1990) and Karlin et al.,Proc. Natl. Acad. Sci. USA 90, 5873-5787 (1993). A particularly usefulBLAST program is the WU-BLAST-2 program which was obtained from Altschulet al., Methods in Enzymology, 266, 460-480 (1996);http://blast.wustl/edu/blast/README.html. WU-BLAST-2 uses several searchparameters, which are optionally set to the default values. Theparameters are dynamic values and are established by the program itselfdepending upon the composition of the particular sequence andcomposition of the particular database against which the sequence ofinterest is being searched; however, the values may be adjusted toincrease sensitivity. Further, an additional useful algorithm is gappedBLAST as reported by Altschul et al, (1997) Nucleic Acids Res. 25,3389-3402. As used herein, the terms “dicot” or “dicotyledon” or“dicotyledonous” refer to a flowering plant whose embryos have two seedleaves or cotyledons. Examples of dicots include, but are not limitedto, Arabidopsis, tobacco, tomato, potato, sweet potato, cassava,alfalfa, lima bean, pea, chick pea, soybean, carrot, strawberry,lettuce, oak, maple, walnut, rose, mint, squash, daisy, Quinoa,buckwheat, mung bean, cow pea, lentil, lupin, peanut, fava bean, Frenchbeans (i.e., common beans), mustard, or cactus.

The terms “monocot” or “monocotyledon” or “monocotyledonous” refer to aflowering plant whose embryos have one cotyledon or seed leaf. Examplesof monocots include, but are not limited to turf grass, maize (corn),rice, oat, wheat, barley, sorghum, orchid, iris, lily, onion, palm, andduckweed.

As used herein, a “low lactose product” is any food compositionconsidered by the FDA to be “lactose reduced”, “low lactose”, or“lactose free”.

Unstructured Milk Proteins

The fusion proteins described herein may comprise one or moreunstructured milk proteins. As used herein the term “milk protein”refers to any protein, or fragment or variant thereof, that is typicallyfound in one or more mammalian milks. Examples of mammalian milkinclude, but are not limited to, milk produced by a cow, human, goat,sheep, camel, horse, donkey, dog, cat, elephant, monkey, mouse, rat,hamster, guinea pig, whale, dolphin, seal, sheep, buffalo, waterbuffalo, dromedary, llama, yak, zebu, reindeer, mole, otter, weasel,wolf, raccoon, walrus, polar bear, rabbit, or giraffe.

An “unstructured milk protein” is a milk protein that lacks a definedsecondary structure, a defined tertiary structure, or a definedsecondary and tertiary structure. Whether a milk protein is unstructuredmay be determined using a variety of biophysical and biochemical methodsknown in the art, such as small angle X-ray scattering, Raman opticalactivity, circular dichroism, nuclear magnetic resonance (NMR) andprotease sensitivity. In some embodiments, a milk protein is consideredto be unstructured if it is unable to be crystallized using standardtechniques.

Illustrative unstructured milk proteins that may be used in the fusionproteins of the disclosure includes members of the casein family ofproteins, such as α-S1 casein, α-S2 casein, β-casein, and κ-casein. Thecaseins are phosphoproteins, and make up approximately 80% of theprotein content in bovine milk and about 20-45% of the protein in humanmilk. Caseins form a multi-molecular, granular structure called a caseinmicelle in which some enzymes, water, and salts, such as calcium andphosphorous, are present. The micellar structure of casein in milk issignificant in terms of a mode of digestion of milk in the stomach andintestine and a basis for separating some proteins and other componentsfrom cow milk. In practice, casein proteins in bovine milk can beseparated from whey proteins by acid precipitation of caseins, bybreaking the micellar structure by partial hydrolysis of the proteinmolecules with proteolytic enzymes, or microfiltration to separate thesmaller soluble whey proteins from the larger casein micelle. Caseinsare relatively hydrophobic, making them poorly soluble in water.

In some embodiments, the casein proteins described herein (e.g., α-S1casein, α-S2 casein, β-casein, and/or κ-casein) are isolated or derivedfrom cow (Bos taurus), goat (Capra hircus), sheep (Ovis aries), waterbuffalo (Bubalus bubalis), dromedary camel (Camelus dromedaries),bactrian camel (Camelus bactrianus), wild yak (Bos mutus), horse (Equuscaballus), donkey (Equus asinus), reindeer (Rangifer tarandus), eurasianelk (Alces alces), alpaca (Vicugna pacos), zebu (Bos indicus), llama(Lama glama), or human (Homo sapiens). In some embodiments, a caseinprotein (e.g., α-S1 casein, α-S2 casein, β-casein, or κ-casein) has atleast 80%, at least 85%, at least 90%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identity with a casein proteinfrom one or more of cow (Bos taurus), goat (Capra hircus), sheep (Ovisaries), water buffalo (Bubalus bubalis), dromedary camel (Camelusdromedaries), bactrian camel (Camelus bactrianus), wild yak (Bos mutus),horse (Equus caballus), donkey (Equus asinus), reindeer (Rangifertarandus), eurasian elk (Alces alces), alpaca (Vicugna pacos), zebu (Bosindicus), llama (Lama glama), or human (Homo sapiens).

As used herein, the term “α-S1 casein” refers to not only the α-S1casein protein, but also fragments or variants thereof. α-S1 casein isfound in the milk of numerous different mammalian species, includingcow, goat, and sheep. The sequence, structure and physical/chemicalproperties of α-S1 casein derived from various species is highlyvariable. An exemplary sequence for bovine α-S1 casein can be found atUniprot Accession No. P02662, and an exemplary sequence for goat α-S1casein can be found at GenBank Accession No. X59836.1.

As used herein, the term “α-S2 casein” refers to not only the α-S2casein protein, but also fragments or variants thereof α-S2 is known asepsilon-casein in mouse, gamma-casein in rat, and casein-A in guineapig. The sequence, structure and physical/chemical properties of α-S2casein derived from various species is highly variable. An exemplarysequence for bovine α-S2 casein can be found at Uniprot Accession No.P02663, and an exemplary sequence for goat α-S2 casein can be found atUniprot Accession No. P33049.

As used herein, the term “β-casein” refers to not only the β-caseinprotein, but also fragments or variants thereof. For example, A1 and A2β-casein are genetic variants of the β-casein milk protein that differby one amino acid (at amino acid 67, A2 β-casein has a proline, whereasA1 has a histidine). Other genetic variants of β-casein include the A3,B, C, D, E, F, H1, H2, I and G genetic variants. The sequence, structureand physical/chemical properties of β-casein derived from variousspecies is highly variable. Exemplary sequences for bovine β-casein canbe found at Uniprot Accession No. P02666 and GenBank Accession No.M15132.1.

As used herein, the term “κ-casein” refers to not only the κ-caseinprotein, but also fragments or variants thereof. κ-casein is cleaved byrennet, which releases a macropeptide from the C-terminal region. Theremaining product with the N-terminus and two-thirds of the originalpeptide chain is referred to as para-κ-casein. The sequence, structureand physical/chemical properties of κ-casein derived from variousspecies is highly variable. Exemplary sequences for bovine κ-casein canbe found at Uniprot Accession No. P02668 and GenBank Accession No.CAA25231.

In some embodiments, the unstructured milk protein is a casein protein,for example, α-S1 casein, α-S2 casein, β-casein, and or κ-casein. Insome embodiments, the unstructured milk protein is κ-casein andcomprises the sequence of SEQ ID NO: 4, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto. In some embodiments, the unstructured milk protein ispara-κ-casein and comprises the sequence of SEQ ID NO: 2, or a sequenceat least 90%, at least 95%, at least 96%, at least 97%, at least 98%, orat least 99% identical thereto. In some embodiments, the unstructuredmilk protein is β-casein and comprises the sequence of SEQ ID NO: 6, ora sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto. In some embodiments, theunstructured milk protein is α-S1 casein and comprises the sequence SEQID NO: 8, or a sequence at least 90%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical thereto. In someembodiments, unstructured milk protein is α-S2 casein and comprises thesequence SEQ ID NO: 84, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto.

In some embodiments, the unstructured milk protein comprises a sequencethat is at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:4. In some embodiments, the unstructured milk protein comprises asequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 2. In some embodiments, the unstructured milk protein comprises asequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 6. In some embodiments, the unstructured milk protein comprises asequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 8. In some embodiments, the unstructured milk protein comprises asequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 84.

In some embodiments, α-S1 casein is encoded by the sequence of SEQ IDNO: 7, or a sequence at least 90%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical thereto. In someembodiments, α-S2 casein is encoded by the sequence of SEQ ID NO: 83, ora sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto. In some embodiments,β-casein is encoded by the sequence of SEQ ID NO: 5, or a sequence atleast 90%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% identical thereto. In some embodiments, κ-casein is encoded bythe sequence of SEQ ID NO: 3, or a sequence at least 90%, at least 95%,at least 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, para-κ-casein is encoded by the sequenceof SEQ ID NO: 1, or a sequence at least 90%, at least 95%, at least 96%,at least 97%, at least 98%, or at least 99% identical thereto.

In some embodiments, the unstructured milk protein is encoded by asequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 7. In some embodiments, the unstructured milk protein is encodedby a sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, or at least 99% identicalto SEQ ID NO: 83. In some embodiments, the unstructured milk protein isencoded by a sequence that is at least 50%, at least 55%, at least 60%,at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical to SEQ ID NO: 3. In some embodiments, the unstructured milkprotein is encoded by a sequence that is at least 50%, at least 55%, atleast 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% identical to SEQ ID NO: 1. In some embodiments, theunstructured milk protein is encoded by a sequence that is at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical to SEQ ID NO: 5.

In some embodiments, the unstructured milk protein is a casein protein,and comprises a sequence that is at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least99% identical to any one of SEQ ID NO: 85-133. In some embodiments, theunstructured milk protein is a casein protein and comprises the sequenceof any one of SEQ ID NO: 85-133.

In some embodiments, the unstructured milk protein comprises a sequencethat is at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical to any one ofSEQ ID NO: 85-98. In some embodiments, the unstructured milk proteincomprises the sequence of any one of SEQ ID NO: 85-98.

In some embodiments, the unstructured milk protein comprises a sequencethat is at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical to any one ofSEQ ID NO: 99-109. In some embodiments, the unstructured milk proteincomprises the sequence of any one of SEQ ID NO: 99-109.

In some embodiments, the unstructured milk protein comprises a sequencethat is at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical to any one ofSEQ ID NO: 110-120. In some embodiments, the unstructured milk proteincomprises the sequence of any one of SEQ ID NO: 110-120.

In some embodiments, the unstructured milk protein comprises a sequencethat is at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical to any one ofSEQ ID NO: 121-133. In some embodiments, the unstructured milk proteincomprises the sequence of any one of SEQ ID NO: 121-133.

Structured Proteins

The fusion proteins described herein may comprise one or more structuredproteins, including any fragment or variant thereof. The proteins maybe, for example, structured animal proteins, or structured plantproteins. In some embodiments, the structured animal proteins aremammalian proteins. In some embodiments, the structured animal proteinsare avian proteins. In some embodiments, the structured proteins arestructured milk proteins.

Whether a milk protein is structured may be determined using a varietyof biophysical and biochemical methods known in the art, such as smallangle X-ray scattering, Raman optical activity, circular dichroism, andprotease sensitivity. In some embodiments, a milk protein is consideredto be structured if it has been crystallized or if it may becrystallized using standard techniques.

In some embodiments, the structured protein is not a protein that istypically used as a marker. As used herein, the term “marker” refers toa protein that produces a visual or other signal and is used to detectsuccessful delivery of a vector (e.g., a DNA sequence) into a cell.Proteins typically used as a marker may include, for example,fluorescent proteins (e.g., green fluorescent protein (GFP)) andbacterial or other enzymes (e.g., β-glucuronidase (GUS),β-galactosidase, luciferase, chloramphenicol acetyltransferase). In someembodiments, the structured protein is a non-marker protein.

A non-limiting list of illustrative structured proteins that may be usedin the fusion proteins described herein is provided in Table 1. In someembodiments, a fragment or variant of any one of the proteins listed inTable 1 may be used. In some embodiments, the structured protein may bean animal protein. For example, in some embodiments, the structuredprotein may be a mammalian protein. In some embodiments, the structuredprotein may be a plant protein. For example, the plant protein may be aprotein that is not typically expressed in a seed. In some embodiments,the plant protein may be a storage protein, e.g., a protein that acts asa storage reserve for nitrogen, carbon, and/or sulfur. In someembodiments, the plant protein may inhibit one or more proteases. Insome embodiments, the structured protein may be a fungal protein.

TABLE 1 Structured proteins Protein or Protein Exemplary UniprotCategories family Native Species Accession No. MammalianAlpha-lactalbumin Bovine (Bos taurus) P00711 Beta-lactoglobulin Bovine(Bos taurus) P02754 Albumin Bovine (Bos taurus) P02769 Lysozyme Bovine(Bos taurus) Q6B411 Collagen family Human (Homo sapiens) Q02388, P02452,P08123, P02458 Hemoglobin Bovine (Bos taurus) P02070 Avian proteinsOvalbumin Chicken (Gallus gallus) P01012 Ovotransferrin Chicken (Gallusgallus) P02789 Ovoglobulin Chicken (Gallus gallus) I0J170 LysozymeChicken (Gallus gallus) P00698 Plant Proteins Oleosins Soybean (Glycinemax) P29530, P29531 Leghemoglobin Soybean (Glycine max) Q41219Extensin-like protein Soybean (Glycine soja) A0A445JU93 family ProlamineRice (Oryza sativa) Q0DJ45 Glutenin Wheat (Sorghum bicolor P10388Gamma-kafirin Wheat (Sorghum bicolor Q41506 preprotein Alpha globulinRice (Oryza sativa) P29835 Basic 7S globulin Soybean (Glycine max)P13917 precursor 2S albumin Soybean (Glycine max) P19594Beta-conglycinins Soybean (Glycine max) P0DO16, P0DO15, P0DO15 GlycininsSoybean (Glycine max) P04347, P04776, P04405 Canein Sugar cane(Saccharum ABP64791.1 officinarum) Zein Corn (Zea Mays) ABP64791.1Patatin Tomato (Solanum P07745 lycopersicum) Kunitz-Trypsin Soybean(Glycine max) Q39898 inhibitor Bowman-Birk Soybean (Glycine max) I1MQD2inhibitor Cystatine Tomato (Solanum Q95E07 lycopersicum) Fungal proteinsHydrophobin I Fungus (Trichoderma reesei) P52754 Hydrophobin II Fungus(Trichoderma reesei) P79073

In some embodiments, the structured protein is an animal protein. Insome embodiments, the structured protein is a mammalian protein. Forexample, the structured protein may be a mammalian protein selectedfrom: β-lactoglobulin, α-lactalbumin, albumin, lysozyme, lactoferrin,lactoperoxidase, hemoglobin, collagen, and an immunoglobulin (e.g., IgA,IgG, IgM, IgE). In some embodiments, the structured mammalian protein isβ-lactoglobulin and comprises the sequence of SEQ ID NO: 10, or asequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto. In some embodiments, thestructured mammalian protein is β-lactoglobulin and is encoded by thesequence of any one of SEQ ID NO: 9, 11, 12, or 13, or a sequence atleast 90%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% identical to any one of SEQ ID NO: 9, 11, 12, or 13. In someembodiments, the structured protein is an avian protein. For example,the structured protein may be an avian protein selected from: ovalbumin,ovotransferrin, lysozyme and ovoglobulin.

In some embodiments, the structured protein is a plant protein. Forexample, the structured protein may be a plant protein selected from:hydrophobin I, hydrophobin II, oleosins, leghemoglobin, extension-likeprotein family, prolamine, glutenin, gamma-kafirin preprotein,α-globulin, basic 7S globulin precursor, 2S albumin, β-conglycinins,glycinins, canein, zein, patatin, kunitz-trypsin inhibitor, bowman-birkinhibitor, and cystatine.

Fusion Proteins Fusion Proteins Comprising an Unstructured Milk Proteinand a Structured Animal (e.g., Mammalian) Protein

In some embodiments, the fusion proteins described herein comprise (i)an unstructured milk protein, and (ii) a structured animal protein. Insome embodiments, the fusion proteins described herein comprise (i) anunstructured milk protein, and (ii) a structured mammalian protein. Insome embodiments, the fusion proteins described herein comprise (i) anunstructured milk protein, and (ii) a structured avian protein. In someembodiments, the fusion proteins described herein comprise (i) anunstructured milk protein, and (ii) a structured fungal protein.

In some embodiments, the fusion proteins comprise an unstructured milkprotein, such as a casein protein. In some embodiments, the fusionproteins comprise an unstructured milk protein selected from α-S1casein, α-S2 casein, β-casein, and κ-casein. In some embodiments, thefusion proteins comprise an unstructured milk protein isolated orderived from cow (Bos taurus), goat (Capra hircus), sheep (Ovis aries),water buffalo (Bubalus bubalis), dromedary camel (Camelus dromedaries),bactrian camel (Camelus bactrianus), wild yak (Bos mutus), horse (Equuscaballus), donkey (Equus asinus), reindeer (Rangifer tarandus), eurasianelk (Alces alces), alpaca (Vicugna pacos), zebu (Bos indicus), llama(Lama glama), or human (Homo sapiens). In some embodiments, the fusionproteins comprise a casein protein (e.g., α-S1 casein, α-S2 casein,β-casein, or κ-casein) from cow (Bos taurus), goat (Capra hircus), sheep(Ovis aries), water buffalo (Bubalus bubalis), dromedary camel (Camelusdromedaries), bactrian camel (Camelus bactrianus), wild yak (Bos mutus),horse (Equus caballus), donkey (Equus asinus), reindeer (Rangifertarandus), eurasian elk (Alces alces), alpaca (Vicugna pacos), zebu (Bosindicus), llama (Lama glama), or human (Homo sapiens).

In some embodiments, the unstructured milk protein is α-S1 casein. Insome embodiments, the unstructured milk protein is α-S1 casein andcomprises the sequence SEQ ID NO: 8, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto. In some embodiments, the unstructured milk protein isα-S1 casein and comprises the sequence of any one of SEQ ID NO: 99-109,or a sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto

In some embodiments, the unstructured milk protein is α-S2 casein. Insome embodiments, the unstructured milk protein is α-S2 casein andcomprises the sequence SEQ ID NO: 84, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto. In some embodiments, the unstructured milk protein isα-S2 casein and comprises the sequence of any one of SEQ ID NO: 110-120,or a sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto.

In some embodiments, the unstructured milk protein is β-casein. In someembodiments, the unstructured milk protein is β-casein and comprises thesequence of SEQ ID NO: 6, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, the unstructured milk protein is β-caseinand comprises the sequence of any one of SEQ ID NO: 121-133, or asequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto.

In some embodiments, the unstructured milk protein is κ-casein. In someembodiments, the unstructured milk protein is κ-casein and comprises thesequence of SEQ ID NO: 4, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, the unstructured milk protein is κ-caseinand comprises the sequence of any one of SEQ ID NO: 85-98, or a sequenceat least 90%, at least 95%, at least 96%, at least 97%, at least 98%, orat least 99% identical thereto.

In some embodiments, the unstructured milk protein is para-κ-casein. Insome embodiments, the unstructured milk protein is para-κ-casein andcomprises the sequence of SEQ ID NO: 2, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto.

In some embodiments, the structured mammalian protein isβ-lactoglobulin, α-lactalbumin, albumin, lysozyme, lactoferrin,lactoperoxidase, hemoglobin, collagen, or an immunoglobulin (e.g., IgA,IgG, IgM, or IgE). In some embodiments, the structured avian protein isovalbumin, ovotransferrin, lysozyme or ovoglobulin.

In some embodiments, the structured mammalian protein isβ-lactoglobulin. In some embodiments, the structured mammalian proteinis β-lactoglobulin and comprises the sequence of SEQ ID NO: 10, or asequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto.

In some embodiments, a fusion protein comprises a casein protein (e.g.,κ-casein, para-κ-casein, β-casein, or α-S1 casein) and β-lactoglobulin.In some embodiments, a fusion protein comprises κ-casein andβ-lactoglobulin (see, e.g., FIG. 3, FIG. 8, FIG. 10A-10B). In someembodiments, a fusion protein comprises para-κ-casein andβ-lactoglobulin (see, e.g., FIG. 6, FIG. 7, FIG. 10A-10B). In someembodiments, a fusion protein comprises β-casein and (3-lactoglobulin.In some embodiments, a fusion protein comprises α-S1 casein andβ-lactoglobulin.

In some embodiments, a plant-expressed recombinant fusion proteincomprises κ-casein, or fragment thereof; and β-lactoglobulin, orfragment thereof. In some embodiments, the fusion protein comprises, inorder from N-terminus to C-terminus, the κ-casein and theβ-lactoglobulin.

Fusion Protein Comprising an Unstructured Milk Protein and a StructuredPlant Protein

In some embodiments, the fusion proteins described herein comprise (i)an unstructured milk protein, and (ii) a structured plant protein. Insome embodiments, the unstructured milk protein is a casein protein,such as α-S1 casein, α-S2 casein, β-casein, or κ-casein. In someembodiments, the plant protein is selected from the group consisting of:hydrophobin I, hydrophobin II, oleosins, leghemoglobin, extension-likeprotein family, prolamine, glutenin, gamma-kafirin preprotein,α-globulin, basic 7S globulin precursor, 2S albumin, β-conglycinins,glycinins, canein, zein, patatin, kunitz-trypsin inhibitor, bowman-birkinhibitor, and cystatine.

Fusion Protein Structure

The fusion proteins described herein may have various differentstructures, in order to increase expression and/or accumulation in aplant or other host organism or cell. In some embodiments, a fusionprotein comprises, in order from N-terminus to C-terminus, anunstructured milk protein and a structured animal (e.g., mammalian oravian) protein. In some embodiments, a fusion protein comprises, inorder from N-terminus to C-terminus, a structured animal (e.g.,mammalian or avian) protein and a milk protein. For example, in someembodiments, a fusion protein comprises, in order from N-terminus toC-terminus κ-casein and β-lactoglobulin. In some embodiments, a fusionprotein comprises, in order from N-terminus to C-terminusβ-lactoglobulin and κ-casein. In some embodiments, a fusion proteincomprises, in order from N-terminus to C-terminus, para-κ-casein andβ-lactoglobulin. In some embodiments, a fusion protein comprises, inorder from N-terminus to C-terminus, β-lactoglobulin and para-κ-casein.In some embodiments, a fusion protein comprises, in order fromN-terminus to C-terminus, β-casein and β-lactoglobulin. In someembodiments, a fusion protein comprises, in order from N-terminus toC-terminus, β-lactoglobulin and β-casein. In some embodiments, a fusionprotein comprises, in order from N-terminus to C-terminus, α-S1 caseinand β-lactoglobulin. In some embodiments, a fusion protein comprises, inorder from N-terminus to C-terminus, β-lactoglobulin and α-S1 casein.

In some embodiments, a fusion protein comprises, in order fromN-terminus to C-terminus, an unstructured milk protein and a structuredplant protein. In some embodiments, a fusion protein comprises, in orderfrom N-terminus to C-terminus, a structured plant protein and a milkprotein. In some embodiments, a fusion protein comprises, in order fromN-terminus to C-terminus, a casein protein and a structured plantprotein. In some embodiments, a fusion protein comprises, in order fromN-terminus to C-terminus, a structured plant protein and a caseinprotein.

In some embodiments, a fusion protein comprises a protease cleavagesite. For example, in some embodiments, the fusion protein comprises anendoprotease, endopeptidase, and/or endoproteinase cleavage site. Insome embodiments, the fusion protein comprises a rennet cleavage site.In some embodiments, the fusion protein comprises a chymosin cleavagesite. In some embodiments, the fusion protein comprises a trypsincleavage site.

The protease cleavage site may be located between the unstructured milkprotein and the structured animal (e.g., mammalian or avian) protein, orbetween the unstructured milk protein and the structured plant protein,such that cleavage of the protein at the protease cleavage site willseparate the unstructured milk protein from the structured animal (e.g.,mammalian or avian) or plant protein.

In some embodiments, the protease cleavage site may be contained withinthe sequence of either the milk protein or the structured animal (e.g.,mammalian or animal) or plant protein. In some embodiments, the proteasecleavage site may be added separately, for example, between the twoproteins.

In some embodiments, a fusion protein comprises a linker between theunstructured milk protein and the structured animal (e.g., mammalian oravian) protein, or between the unstructured milk protein and thestructured plant protein. In some embodiments, the linker may comprise apeptide sequence recognizable by an endoprotease. In some embodiments,the linker may comprise a protease cleavage site. In some embodiments,the linker may comprise a self-cleaving peptide, such as a 2A peptide.

In some embodiments, a fusion protein may comprise a signal peptide. Thesignal peptide may be cleaved from the fusion protein, for example,during processing or transport of the protein within the cell. In someembodiments, the signal peptide is located at the N-terminus of thefusion protein. In some embodiments, the signal peptide is located atthe C-terminus of the fusion protein.

In some embodiments, the signal peptide is selected from the groupconsisting of GmSCB1, StPat21, 2Sss, Sig2, Sig12, Sig8, Sig10, Sig11,and Coixss. In some embodiments, the signal peptide is Sig10 andcomprises SEQ ID NO: 15, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, the signal peptide is Sig2 and comprisesSEQ ID NO: 17, or a sequence at least 90%, at least 95%, at least 96%,at least 97%, at least 98%, or at least 99% identical thereto.

In some embodiments, the fusion protein comprises the sequence of SEQ IDNO: 71. In some embodiments, the fusion protein comprises the sequenceof SEQ ID NO: 73. In some embodiments, the fusion protein comprises thesequence of SEQ ID NO: 75. In some embodiments, the fusion proteincomprises the sequence of SEQ ID NO: 77. In some embodiments, the fusionprotein comprises the sequence of SEQ ID NO: 79. In some embodiments,the fusion protein comprises the sequence of SEQ ID NO: 81. In someembodiments, the fusion protein comprises the sequence of SEQ ID NO:135. In some embodiments, the fusion protein comprises the sequence ofSEQ ID NO: 137.

In some embodiments, the fusion protein comprises the sequence of SEQ IDNO: 71, with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino acidsubstitutions. In some embodiments, the fusion protein comprises thesequence of SEQ ID NO: 73, with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moreamino acid substitutions. In some embodiments, the fusion proteincomprises the sequence of SEQ ID NO: 75, with 1, 2, 3, 4, 5, 6, 7, 8, 9,10, or more amino acid substitutions. In some embodiments, the fusionprotein comprises the sequence of SEQ ID NO: 77, with 1, 2, 3, 4, 5, 6,7, 8, 9, 10, or more amino acid substitutions. In some embodiments, thefusion protein comprises the sequence of SEQ ID NO: 79, with 1, 2, 3, 4,5, 6, 7, 8, 9, 10, or more amino acid substitutions. In someembodiments, the fusion protein comprises the sequence of SEQ ID NO: 81,with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino acid substitutions. Insome embodiments, the fusion protein comprises the sequence of SEQ IDNO: 135, with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino acidsubstitutions. In some embodiments, the fusion protein comprises thesequence of SEQ ID NO: 137, with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moreamino acid substitutions.

In some embodiments, the fusion protein comprises the sequence of SEQ IDNO: 71, or a sequence at least 90%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical thereto. In someembodiments, the fusion protein comprises the sequence of SEQ ID NO: 73,or a sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto. In some embodiments, thefusion protein comprises the sequence of SEQ ID NO: 75, or a sequence atleast 90%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% identical thereto. In some embodiments, the fusion proteincomprises the sequence of SEQ ID NO: 77, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto. In some embodiments, the fusion protein comprises thesequence of SEQ ID NO: 79, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, the fusion protein comprises the sequenceof SEQ ID NO: 81, or a sequence at least 90%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% identical thereto. Insome embodiments, the fusion protein comprises the sequence of SEQ IDNO: 135, or a sequence at least 90%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical thereto. In someembodiments, the fusion protein comprises the sequence of SEQ ID NO:137, or a sequence at least 90%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical thereto.

In some embodiments, the fusion proteins have a molecular weight in therange of about 1 kDa to about 500 kDa, about 1 kDa to about 250 kDa,about 1 to about 100 kDa, about 10 to about 50 kDa, about 1 to about 10kDa, about 10 to about 200 kDa, about 30 to about 150 kDa, about 30 kDato about 50 kDa, or about 20 to about 80 kDa.

Nucleic Acids Encoding Fusion Proteins and Vectors Comprising the Same

Also provided herein are nucleic acids encoding the fusion proteins ofthe disclosure, for example fusion proteins comprising an unstructuredmilk protein and a structured animal (e.g., mammalian or avian) or plantprotein. In some embodiments, the nucleic acids are DNAs. In someembodiments, the nucleic acids are RNAs.

In some embodiments, a nucleic acid comprises a sequence encoding afusion protein. In some embodiments, a nucleic acid comprises a sequenceencoding a fusion protein, which is operably linked to a promoter. Insome embodiments, a nucleic acid comprises, in order from 5′ to 3′, apromoter, a 5′ untranslated region (UTR), a sequence encoding a fusionprotein, and a terminator.

The promoter may be a plant promoter. A “plant promoter” is a promotercapable of initiating transcription in plant cells. Examples ofpromoters under developmental control include promoters thatpreferentially initiate transcription in certain organs, such as leaves,roots, flowers, seeds and tissues such as fibers, xylem vessels,tracheids, or sclerenchyma. Such promoters are referred to as“tissue-preferred.” Promoters which initiate transcription only incertain tissue are referred to as “tissue-specific.” A “cell-type”specific promoter primarily drives expression in certain cell types inone or more organs, for example, vascular cells in leaves, roots,flowers, or seeds. An “inducible” promoter is a promoter which is underenvironmental control. Examples of environmental conditions that mayaffect transcription by inducible promoters include anaerobic conditionsor the presence of light. Tissue-specific, tissue-preferred, cell-typespecific, and inducible promoters constitute the class of“non-constitutive” promoters. A “constitutive” promoter is a promoterwhich is active under most environmental conditions.

In some embodiments, the promoter is a plant promoter derived from, forexample soybean, lima bean, Arabidopsis, tobacco, rice, maize, barley,sorghum, wheat, pea, and/or oat. In some embodiments, the promoter is aconstitutive or an inducible promoter. Exemplary constitutive promotersinclude, but are not limited to, the promoters from plant viruses suchas the 35S promoter from CaMV and the promoters from such genes as riceactin; ubiquitin; pEMU; MAS and maize H3 histone. In some embodiments,the constitutive promoter is the ALS promoter, Xbal/Ncol fragment 5′ tothe Brassica napus ALS3 structural gene (or a nucleotide sequencesimilarity to said Xbal/Ncol fragment).

In some embodiments, the promoter is a plant tissue-specific ortissue-preferential promoter. In some embodiments, the promoter isisolated or derived from a soybean gene. Illustrative soybeantissue-specific promoters include AR-Pro1, AR-Pro2, AR-Pro3, AR-Pro4,AR-Pro5, AR-Pro6, AR-Pro7, AR-Pro8, and AR-Pro9.

In some embodiments, the plant is a seed-specific promoter. In someembodiments, the seed-specific promoter is selected from the groupconsisting of PvPhas, BnNap, AtOle1, GmSeed2, GmSeed3, GmSeed5, GmSeed6,GmSeed7, GmSeed8, GmSeed10, GmSeed11, GmSeed12, pBCON, GmCEP1-L, GmTHIC,GmBg7S1, GmGRD, GmOLEA, GmOLER, Gm2S-1, and GmBBld-II. In someembodiments, the seed-specific promoter is PvPhas and comprises thesequence of SEQ ID NO: 18, or a sequence at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identicalthereto. In some embodiments, the seed-specific promoter is GmSeed2 andcomprises the sequence of SEQ ID NO: 19, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto. In some embodiments, the promoter is a CauliflowerMosaic Virus (CaMV) 35S promoter.

In some embodiments, the promoter is a soybean polyubiquitin (Gmubi)promoter, a soybean heat shock protein 90-like (GmHSP90L) promoter, asoybean Ethylene Response Factor (GmERF) promoter. In some embodiments,the promoter is a constitutive soybean promoter derived from GmScreamM1,GmScreamM4, GmScreamM8 genes or GmubiXL genes.

In some embodiments, the 5′ UTR is selected from the group consisting ofArc5′UTR and glnB1UTR. In some embodiments, the 5′ untranslated regionis Arc5′UTR and comprises the sequence of SEQ ID NO: 20, or a sequenceat least 90%, at least 95%, at least 96%, at least 97%, at least 98%, orat least 99% identical thereto.

In some embodiments, the terminator sequence is isolated or derived froma gene encoding Nopaline synthase, Arc5-1, an Extensin, Rb7 matrixattachment region, a Heat shock protein, Ubiquitin 10, Ubiquitin 3, andM6 matrix attachment region. In some embodiments, the terminatorsequence is isolated or derived from a Nopaline synthase gene andcomprises the sequence of SEQ ID NO: 22, or a sequence at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%identical thereto.

In some embodiments, the nucleic acid comprises a 3′ UTR. For example,the 3′ untranslated region may be Arc5-1 and comprise SEQ ID NO: 21, ora sequence at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, or at least 99% identical thereto.

In some embodiments the nucleic acid comprises a gene encoding aselectable marker. One illustrative selectable marker gene for planttransformation is the neomycin phosphotransferase II (nptll) gene,isolated from transposon Tn5, which, when placed under the control ofplant regulatory signals, confers resistance to kanamycin. Anotherexemplary marker gene is the hygromycin phosphotransferase gene whichconfers resistance to the antibiotic hygromycin. In some embodiments,the selectable marker is of bacterial origin and confers resistance toantibiotics such as gentamycin acetyl transferase, streptomycinphosphotransferase, and aminoglycoside-3′-adenyl transferase, thebleomycin resistance determinant. In some embodiments, the selectablemarker genes confer resistance to herbicides such as glyphosate,glufosinate or bromoxynil. In some embodiments, the selectable marker ismouse dihydrofolate reductase, plant 5-enolpyruvylshikimate-3-phosphatesynthase and plant acetolactate synthase. In some embodiments, theselectable marker is acetolactate synthase (e.g., AtCsr1.2).

In some embodiments, a nucleic acid comprises an endoplasmic reticulumretention signal. For example, in some embodiments, a nucleic acidcomprises a KDEL sequence (SEQ ID NO: 23). In some embodiments, thenucleic acid may comprise an endoplasmic reticulum retention signalselected from any one of SEQ ID NO: 23-70.

Shown in Table 2 are exemplary promoters, 5′ UTRs, signal peptides, andterminators that may be used in the nucleic acids of the disclosure.

TABLE 2 Promoters, 5′ UTRs, signal peptides and terminators IllustrativeAccession No. Type Name Description Native Species (Glyma, GenBank)Promoter PvPhas Phaseolin-1 (aka β-phaseolin) Common bean J01263.1(Phaseolus vulgaris) BnNap Napin-1 Rapeseed (Brassica J02798.1 napus)AtOle1 Oleosin-1 (Ole1) Arabidopsis (Arabidopsis X62353.1, thaliana)AT4G25140 GmSeed2 Gy1 (Glycinin 1) Soybean (Glycine max) Glyma.03G163500GmSeed3 cysteine protease Soybean (Glycine max) Glyma.08G116300 GmSeed5Gy5 (Glycinin 5) Soybean (Glycine max) Glyma.13G123500 GmSeed6 Gy4(Glycinin 4) Soybean (Glycine max) Glyma.10G037100 GmSeed7 Kunitztrypsin protease Soybean (Glycine max) Glyma.01G095000 inhibitor GmSeed8mKunitz trypsin protease Soybean (Glycine max) Glyma.08G341500 inhibitorGmSeed10 Legume Lectin Domain Soybean (Glycine max) Glyma.02G012600GmSeed11 β-conglycinin a subunit Soybean (Glycine max) Glyma.20G148400GmSeed12 β-conglycinin a′ subunit Soybean (Glycine max) Glyma.10G246300pBCON β-conglycinin β subunit Soybean (Glycine max) Glyma.20G148200GmCEP1-L KDEL-tailed cysteine Soybean (Glycine max) Glyma06g42780endopeptidase CEP1-like GmTHIC phosphomethylpyrimidine Soybean (Glycinemax) Glyma11g26470 synthase GmBg7S1 Basic 7S globulin precursor Soybean(Glycine max) Glyma03g39940 GmGRD glucose and ribitol Soybean (Glycinemax) Glyma07g38790 dehydrogenase-like GmOLEA Oleosin isoform A Soybean(Glycine max) Glyma.19g063400 GmOLEB Oleosin isoform B Soybean (Glycinemax) Glyma.16g071800 Gm2S-1 2S albumin Soybean (Glycine max)Glyma13g36400 GmBBId-II Bowman-Birk protease Soybean (Glycine max)Glyma16g33400 inhibitor 5′UTR Arc5′UTR arc5-1 gene Phaseolus vulgarisJ01263.1 glnB1UTR 65 bp of native glutamine Soybean (Glycine max)AF301590.1 synthase Signal peptide GmSCB1 Seed coat BURP domain Soybean(Glycine max) Glyma07g28940.1 protein StPat21 Patatin Tomato (SolanumCAA27588 lycopersicum) 2Sss 2S albumin Soybean (Glycine max)Glyma13g36400 Sig2 Glycinin G1 N-terminal Soybean (Glycine max)Glyma.03G163500 peptide Sig12 Beta-conglycinin alpha prime Soybean(Glycine max) Glyma.10G246300 subunit N-terminal peptide Sig8 Kunitztrypsin inhibitor N- Soybean (Glycine max) Glyma.08G341500 terminalpeptide Sig10 Lectin N-terminal peptide Soybean (Glycine max)Glyma.02G012600 from Glycine max Sig11 Beta-conglycinin alpha Soybean(Glycine max) Glyma.20G148400 subunit N-terminal peptide CoixssAlpha-coixin N-terminal peptide from Coix lacryma- Coix lacryma-job jobKDEL C-terminal amino acids of Phaseolus vulgaris sulfhydrylendopeptidase Terminator NOS Nopaline synthase gene Agrobacteriumtermination sequence tumefaciens ARC arc5-1 gene termination Phaseolusvulgaris J01263.1 sequence EU Extensin termination sequence Nicotianatabacum Rb7 Rb7 matrix attachment region Nicotiana tabacum terminationsequence HSP or Heat shock termination Arabidopsis thaliana AtHSPsequence AtUbi10 Ubiquitin 10 termination Arabidopsis thaliana sequenceStubi3 Ubiquitin 3 termination Solanum tuberosum TM6 M6 matrixattachment region Nicotiana tabacum termination sequence

Illustrative nucleic acids of the disclosure are provided in FIG. 1A-1P.In some embodiments a nucleic acid comprises, from 5′ to 3′, a promoter,a 5′UTR, a sequence encoding an unstructured milk protein, a sequenceencoding a structured mammalian protein, an endoplasmic reticulumretention signal, and a terminator (See, e.g., FIG. 1A). In someembodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding an unstructured milk protein, a sequenceencoding a linker, a sequence encoding a structured mammalian protein,an endoplasmic reticulum retention signal, and a terminator (See, e.g.,FIG. 1B). In some embodiments a nucleic acid comprises, from 5′ to 3′, apromoter, a 5′UTR, a sequence encoding an unstructured milk protein, asequence encoding a linker, a sequence encoding a structured mammalianprotein, and a terminator (See, e.g., FIG. 1C). In some embodiments anucleic acid comprises, from 5′ to 3′, a promoter, a 5′UTR, a sequenceencoding an unstructured milk protein, a sequence encoding a structuredmammalian protein, and a terminator (See, e.g., FIG. 1D). In someembodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding a structured mammalian protein, a sequenceencoding an unstructured milk protein, an endoplasmic reticulumretention signal, and a terminator (See, e.g., FIG. 1E). In someembodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding a structured mammalian protein, a sequenceencoding a linker, a sequence encoding an unstructured milk protein, anendoplasmic reticulum retention signal, and a terminator (See, e.g.,FIG. 1F). In some embodiments a nucleic acid comprises, from 5′ to 3′, apromoter, a 5′UTR, a sequence encoding a structured mammalian protein, asequence encoding a linker, a sequence encoding an unstructured milkprotein, and a terminator (See, e.g., FIG. 1G). In some embodiments anucleic acid comprises, from 5′ to 3′, a promoter, a 5′UTR, a sequenceencoding a structured mammalian protein, a sequence encoding anunstructured milk protein, and a terminator (See, e.g., FIG. 1H). Insome embodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding a signal peptide, a sequence encoding anunstructured milk protein, a sequence encoding a structured mammalianprotein, an endoplasmic reticulum retention signal, and a terminator(See, e.g., FIG. 1I). In some embodiments a nucleic acid comprises, from5′ to 3′, a promoter, a 5′UTR, a sequence encoding a signal peptide, asequence encoding an unstructured milk protein, a sequence encoding alinker, a sequence encoding a structured mammalian protein, anendoplasmic reticulum retention signal, and a terminator (See, e.g.,FIG. 1J). In some embodiments a nucleic acid comprises, from 5′ to 3′, apromoter, a 5′UTR, a sequence encoding a signal peptide, a sequenceencoding an unstructured milk protein, a sequence encoding a linker, asequence encoding a structured mammalian protein, and a terminator (See,e.g., FIG. 1K). In some embodiments a nucleic acid comprises, from 5′ to3′, a promoter, a 5′UTR, a sequence encoding a signal peptide, asequence encoding an unstructured milk protein, a sequence encoding astructured mammalian protein, and a terminator (See, e.g., FIG. 1L). Insome embodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding a signal peptide, a sequence encoding astructured mammalian protein, a sequence encoding an unstructured milkprotein, an endoplasmic reticulum retention signal, and a terminator(See, e.g., FIG. 1M). In some embodiments a nucleic acid comprises, from5′ to 3′, a promoter, a 5′UTR, a sequence encoding a signal peptide, asequence encoding a structured mammalian protein, a sequence encoding alinker, a sequence encoding an unstructured milk protein, an endoplasmicreticulum retention signal, and a terminator (See, e.g., FIG. 1N). Insome embodiments a nucleic acid comprises, from 5′ to 3′, a promoter, a5′UTR, a sequence encoding a signal peptide, a sequence encoding astructured mammalian protein, a sequence encoding a linker, a sequenceencoding an unstructured milk protein, and a terminator (See, e.g., FIG.1O). In some embodiments a nucleic acid comprises, from 5′ to 3′, apromoter, a 5′UTR, a sequence encoding a signal peptide, a sequenceencoding a structured mammalian protein, a sequence encoding anunstructured milk protein, and a terminator (See, e.g., FIG. 1P).

In some embodiments, the nucleic acid comprises an expression cassettecomprising a OKC1-T:OLG1 (Optimized Kappa Casein version1:beta-lactoglobulin version 1) fusion driven by PvPhas promoter fusedwith arc5′UTR:sig10, followed by the ER retention signal (KDEL) and the3′UTR of the arc5-1 gene, “arc-terminator” (See, e.g., FIG. 3). In someembodiments, the nucleic acid comprises SEQ ID NO: 72.

In some embodiments, the nucleic acid comprises an expression cassettecomprising a OBC-T2:FM:OLG1 (Optimized Beta Casein Truncated version2:Chymosin cleavage site:beta-lactoglobulin version 1) fusion driven byPvPhas promoter fused with arc5′UTR:sig10, followed by the 3′UTR of thearc5-1 gene, “arc-terminator” (See, e.g., FIG. 4). In some embodiments,the nucleic acid comprises SEQ ID NO: 74. The Beta Casein is “truncated”in that the bovine secretion signal is removed, and replaced with aplant targeting signal.

In some embodiments, the nucleic acid comprises an expression cassettecomprising a OaS1-T:FM:OLG1 (Optimized Alpha S1 Casein Truncated version1:Chymosin cleavage site:beta-lactoglobulin version 1) fusion driven byPvPhas promoter fused with arc5′UTR:sig10, followed by the 3′UTR of thearc5-1 gene, “arc-terminator” (See, e.g., FIG. 5). In some embodiments,the nucleic acid comprises SEQ ID NO: 76. The Alpha S1 is “truncated” inthat the bovine secretion signal is removed, and replaced with a planttargeting signal.

In some embodiments, the nucleic acid comprises an expression cassettecomprising a para-OKC1-T:FM:OLG1:KDEL (Optimized paraKappa Caseinversion 1:Chymosin cleavage site:beta-lactoglobulin version 1) fusiondriven by PvPhas promoter fused with arc5′UTR:sig 10, followed by the ERretention signal (KDEL) and the 3′UTR of the arc5-1 gene,“arc-terminator” (See, e.g., FIG. 6). In some embodiments, the nucleicacid comprises SEQ ID NO: 78.

In some embodiments, the nucleic acid comprises an expression cassettecomprising a para-OKC1-T:FM:OLG1 (Optimized paraKappa Casein version1:Chymosin cleavage site:beta-lactoglobulin version 1) fusion driven byPvPhas promoter fused with arc5′UTR:sig 10, followed by the 3′UTR of thearc5-1 gene, “arc-terminator” (See, e.g., FIG. 7). In some embodiments,the nucleic acid comprises SEQ ID NO: 80.

In some embodiments, the nucleic acid comprises an expression cassettecomprising a OKC1-T-OLG1 (Optimized Kappa Casein version1:beta-lactoglobulin version 1) fusion that is driven by the promoterand signal peptide of glycinin 1 (GmSeed2:sig2) followed by the ERretention signal (KDEL) and the nopaline synthase gene terminationsequence (nos term) (See, e.g., FIG. 8). In some embodiments, thenucleic acid comprises SEQ ID NO: 82. In some embodiments, a nucleicacid encoding a fusion protein comprises the sequence of any one of SEQID NO: 72, 74, 76, 78, 80, 82, 134, or 136.

In some embodiments, the nucleic acids are codon optimized forexpression in a host cell. Codon optimization is a process used toimprove gene expression and increase the translational efficiency of agene of interest by accommodating codon bias of the host organism (i.e.,the organism in which the gene is expressed). Codon-optimized mRNAsequences that are produced using different programs or approaches canvary because different codon optimization strategies differ in how theyquantify codon usage and implement codon changes. Some approaches usethe most optimal (frequently used) codon for all instances of an aminoacid, or a variation of this approach. Other approaches adjust codonusage so that it is proportional to the natural distribution of the hostorganism. These approaches include codon harmonization, which endeavorsto identify and maintain regions of slow translation thought to beimportant for protein folding. Alternative approaches involve usingcodons thought to correspond to abundant tRNAs, using codons accordingto their cognate tRNA concentrations, selectively replacing rare codons,or avoiding occurrences of codon-pairs that are known to translateslowly. In addition to approaches that vary in the extent to which codonusage is considered as a parameter, there are hypothesis-free approachesthat do not consider this parameter. Algorithms for performing codonoptimization are known to those of skill in the art and are widelyavailable on the Internet.

In some embodiments the nucleic acids are codon optimized for expressionin a plant species. The plant species may be, for example, a monocot ora dicot. In some embodiments, the plant species is a dicot speciesselected from soybean, lima bean, Arabidopsis, tobacco, rice, maize,barley, sorghum, wheat and/or oat. In some embodiments, the plantspecies is soybean.

The nucleic acids of the disclosure may be contained within a vector.The vector may be, for example, a viral vector or a non-viral vector. Insome embodiments, the non-viral vector is a plasmid, such as anAgrobacterium Ti plasmid. In some embodiments, the non-viral vector is alipid nanoparticle.

In some embodiments, a vector comprises a nucleic acid encoding arecombinant fusion protein, wherein the recombinant fusion proteincomprises: (i) an unstructured milk protein, and (ii) a structuredanimal (e.g., mammalian or avian) protein. In some embodiments, thevector is an Agrobacterium Ti plasmid.

In some embodiments, a method for expressing a fusion protein in a plantcomprises contacting the plant with a vector of the disclosure. In someembodiments, the method comprises maintaining the plant or part thereofunder conditions in which the fusion protein is expressed.

Plants Expressing Fusion Proteins

Also provided herein are transgenic plants expressing one or more fusionproteins of the disclosure. In some embodiments, the transgenic plantsstably express the fusion protein. In some embodiments, the transgenicplants stably express the fusion protein in the plant in an amount of atleast 1% per the total protein weight of the soluble protein extractablefrom the plant. For example, the transgenic plants may stably expressthe fusion protein in an amount of at least 1%, at least 1.5%, at least2%, at least 2.5%, at least 3%, at least 3.5%, at least 4%, at least4.5%, at least 5%, at least 5.5%, at least 6%, at least 6.5%, at least7%, at least 7.5%, at least 8%, at least 8.5%, at least 9%, at least9.5%, at least 10%, at least 10.5%, at least 11%, at least 11.5%, atleast 12%, at least 12.5%, at least 13%, at least 13.5%, at least 14%,at least 14.5%, at least 15%, at least 15.5%, at least 16%, at least16.5%, at least 17%, at least 17.5%, at least 18%, at least 18.5%, atleast 19%, at least 19.5%, at least 20%, or more of total protein weightof soluble protein extractable from the plant.

In some embodiments, the transgenic plants stably express the fusionprotein in an amount of less than about 1% of the total protein weightof soluble protein extractable from the plant. In some embodiments, thetransgenic plants stably express the fusion protein in the range ofabout 1% to about 2%, about 3% to about 4%, about 4% to about 5%, about5% to about 6%, about 6% to about 7%, about 7% to about 8%, about 8% toabout 9%, about 9% to about 10%, about 10% to about 11%, about 11% toabout 12%, about 12% to about 13%, about 13% to about 14%, about 14% toabout 15%, about 15% to about 16%, about 16% to about 17%, about 17%, toabout 18%, about 18% to about 19%, about 19% to about 20%, or more thanabout 20% of the total protein weight of soluble protein extractablefrom the plant.

In some embodiments, the transgenic plant stably express the fusionprotein in an amount in the range of about 0.5% to about 3%, about 1% toabout 4%, about 1% to about 5%, about 2% to about 5%, about 1% to about10%, about 2% to about 10%, about 3% to about 10%, about 5 to about 12%,about 4% to about 10%, or about 5% to about 10%, about 4% to about 8%,about 5% to about 15%, about 5% to about 18%, about 10% to about 20%, orabout 1% to about 20% of the total protein weight of soluble proteinextractable from the plant.

In some embodiments, the fusion protein is expressed at a level at least2-fold higher than an unstructured milk protein expressed individuallyin a plant. For example, in some embodiments, the fusion protein isexpressed at a level at least 2-fold, at least 2.5-fold, at least3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least5-fold, at least 5.5-fold, at least 6-fold, at least 7-fold, at least7.5-fold, at least 8-fold, at least 8.5-fold, at least 9-fold, at least9.5-fold, at least 10-fold, at least 25-fold, at least 50-fold, or atleast 100-fold higher than an unstructured milk protein expressedindividually in a plant.

In some embodiments, the fusion protein accumulates in the plant atleast 2-fold higher than an unstructured milk protein expressed withoutthe structured animal (e.g., mammalian or avian) protein. For example,in some embodiments, the fusion protein accumulates in the plant atleast 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, atleast 4-fold, at least 4.5-fold, at least 5-fold, at least 5.5-fold, atleast 6-fold, at least 7-fold, at least 7.5-fold, at least 8-fold, atleast 8.5-fold, at least 9-fold, at least 9.5-fold, at least 10-fold, atleast 25-fold, at least 50-fold, or at least 100-fold higher than anunstructured milk protein expressed without the structured animalprotein.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein, wherein thefusion protein comprises (i) an unstructured milk protein, and (ii) astructured animal (e.g., mammalian or avian) protein. In someembodiments, the fusion protein is stably expressed in the plant in anamount of 1% or higher per the total protein weight of the solubleprotein extractable from the plant. In some embodiments, the fusionprotein is stably expressed in the plant in an amount of 2% or higherper the total protein weight of the soluble protein extractable from theplant. In some embodiments, the fusion protein is stably expressed inthe plant in an amount of 3% or higher per the total protein weight ofthe soluble protein extractable from the plant. In some embodiments, thefusion protein is stably expressed in the plant in an amount of 4% orhigher per the total protein weight of the soluble protein extractablefrom the plant. In some embodiments, the fusion protein is stablyexpressed in the plant in an amount of 5% or higher per the totalprotein weight of the soluble protein extractable from the plant. Insome embodiments, the fusion protein is stably expressed in the plant inan amount of 6% or higher per the total protein weight of the solubleprotein extractable from the plant. In some embodiments, the fusionprotein is stably expressed in the plant in an amount of 7% or higherper the total protein weight of the soluble protein extractable from theplant. In some embodiments, the fusion protein is stably expressed inthe plant in an amount of 8% or higher per the total protein weight ofthe soluble protein extractable from the plant. In some embodiments, thefusion protein is stably expressed in the plant in an amount of 9% orhigher per the total protein weight of the soluble protein extractablefrom the plant. In some embodiments, the fusion protein is stablyexpressed in the plant in an amount of 10% or higher per the totalprotein weight of the soluble protein extractable from the plant. Insome embodiments, the fusion protein is stably expressed in the plant inan amount of 11% or higher per the total protein weight of the solubleprotein extractable from the plant. In some embodiments, the fusionprotein is stably expressed in the plant in an amount of 12% or higherper the total protein weight of the soluble protein extractable from theplant. In some embodiments, the fusion protein is stably expressed inthe plant in an amount of 13% or higher per the total protein weight ofthe soluble protein extractable from the plant. In some embodiments, thefusion protein is stably expressed in the plant in an amount of 14% orhigher per the total protein weight of the soluble protein extractablefrom the plant. In some embodiments, the fusion protein is stablyexpressed in the plant in an amount of 15% or higher per the totalprotein weight of the soluble protein extractable from the plant. Insome embodiments, the fusion protein is stably expressed in the plant inan amount of 16% or higher per the total protein weight of the solubleprotein extractable from the plant. In some embodiments, the fusionprotein is stably expressed in the plant in an amount of 17% or higherper the total protein weight of the soluble protein extractable from theplant. In some embodiments, the fusion protein is stably expressed inthe plant in an amount of 18% or higher per the total protein weight ofthe soluble protein extractable from the plant. In some embodiments, thefusion protein is stably expressed in the plant in an amount of 19% orhigher per the total protein weight of the soluble protein extractablefrom the plant. In some embodiments, the fusion protein is stablyexpressed in the plant in an amount of 20% or higher per the totalprotein weight of the soluble protein extractable from the plant.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein, wherein thefusion protein comprises from N-terminus to C-terminus, the unstructuredmilk protein and the animal (e.g., mammalian or avian) protein. In someembodiments, the fusion protein comprises, from N-terminus toC-terminus, the structured animal (e.g., mammalian or avian) protein andthe milk protein.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein, wherein thefusion protein comprises an unstructured milk protein such as a caseinprotein. In some embodiments, a stably transformed plant comprises inits genome: a recombinant DNA construct encoding a fusion protein,wherein the fusion protein comprises an unstructured milk proteinselected from α-S1 casein, α-S2 casein, (3-casein, and κ-casein. In someembodiments, the unstructured milk protein is α-S1 casein. In someembodiments, the unstructured milk protein is α-S1 casein and comprisesthe sequence SEQ ID NO: 8, or a sequence at least 90% identical thereto.In some embodiments, the unstructured milk protein is α-S2 casein. Insome embodiments, the unstructured milk protein is α-S2 casein andcomprises the sequence SEQ ID NO: 84, or a sequence at least 90%identical thereto. In some embodiments, the unstructured milk protein isβ-casein. In some embodiments, the unstructured milk protein is β-caseinand comprises the sequence of SEQ ID NO: 6, or a sequence at least 90%identical thereto. In some embodiments, the unstructured milk protein isκ-casein. In some embodiments, the unstructured milk protein is κ-caseinand comprises the sequence of SEQ ID NO: 4, or a sequence at least 90%identical thereto. In some embodiments, the unstructured milk protein ispara-κ-casein. In some embodiments, the unstructured milk protein ispara-κ-casein and comprises the sequence of SEQ ID NO: 2, or a sequenceat least 90% identical thereto.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein, wherein thefusion protein comprises a structured mammalian protein selected fromβ-lactoglobulin, α-lactalbumin, albumin, lysozyme, lactoferrin,lactoperoxidase, hemoglobin, collagen, and an immunoglobulin (e.g., IgA,IgG, IgM, or IgE). In some embodiments, the structured mammalian proteinis β-lactoglobulin. In some embodiments, the structured mammalianprotein is β-lactoglobulin and comprises the sequence of SEQ ID NO: 10,or a sequence at least 90% identical thereto. In some embodiments, astably transformed plant comprises in its genome: a recombinant DNAconstruct encoding a fusion protein, wherein the fusion proteincomprises a structured avian protein selected from lysozyme, ovalbumin,ovotransferrin, and ovoglobulin.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein, wherein thefusion protein comprises a casein protein and β-lactoglobulin. In someembodiments, a stably transformed plant comprises in its genome: arecombinant DNA construct encoding a fusion protein, wherein the fusionprotein comprises κ-casein and β-lactoglobulin. In some embodiments, thefusion protein comprises para-κ-casein and β-lactoglobulin. In someembodiments, the fusion protein comprises β-casein and β-lactoglobulin.In some embodiments, the fusion protein comprises α-S1 casein andβ-lactoglobulin.

In some embodiments, a stably transformed plant comprises in its genome:a recombinant DNA construct encoding a fusion protein; wherein thefusion protein comprises (1) κ-casein, and (ii) β-lactoglobulin. In someembodiments; and wherein the fusion protein is stably expressed in theplant in an amount of 1% or higher per the total protein weight of thesoluble protein extractable from the plant.

In some embodiments, the stably transformed plant is a monocot. Forexample, in some embodiments, the plant may be a monocot selected fromturf grass, maize (corn), rice, oat, wheat, barley, sorghum, orchid,iris, lily, onion, palm, and duckweed.

In some embodiments, the stably transformed plant is a dicot. Forexample, in some embodiments, the plant may be a dicot selected fromArabidopsis, tobacco, tomato, potato, sweet potato, cassava, alfalfa,lima bean, pea, chick pea, soybean, carrot, strawberry, lettuce, oak,maple, walnut, rose, mint, squash, daisy, Quinoa, buckwheat, mung bean,cow pea, lentil, lupin, peanut, fava bean, French beans (i.e., commonbeans), mustard, or cactus. In some embodiments, the plant is a soybean(Glycine max).

In some embodiments, the plant is a non-vascular plant selected frommoss, liverwort, hornwort or algae. In some embodiments, the plant is avascular plant reproducing from spores (e.g., a fern).

In some embodiments, the recombinant DNA construct is codon-optimizedfor expression in the plant. For example, in some embodiments, therecombinant DNA construct is codon-optimized for expression in a soybeanplant.

The transgenic plants described herein may be generated by variousmethods known in the art. For example, a nucleic acid encoding a fusionprotein may be contacted with a plant, or a part thereof, and the plantmay then be maintained under conditions wherein the fusion protein isexpressed. In some embodiments, the nucleic acid is introduced into theplant, or part thereof, using one or more methods for planttransformation known in the art, such as Agrobacterium-mediatedtransformation, particle bombardment-medicated transformation,electroporation, and microinjection.

In some embodiments, a method for stably expressing a recombinant fusionprotein in a plant comprises (i) transforming a plant with a planttransformation vector comprising an expression cassette comprising: asequence encoding a fusion protein, wherein the fusion protein comprisesan unstructured milk protein, and a structured animal (e.g., mammalianor avian) protein; and (ii) growing the transformed plant underconditions wherein the recombinant fusion protein is expressed. In someembodiments, the recombinant fusion protein is expressed in an amount of1% or higher per the total protein weight of the soluble proteinextractable from the plant. In some embodiments, the unstructured milkprotein is κ-casein. In some embodiments, the structured mammalianprotein is β-lactoglobulin. In some embodiments, the unstructured milkprotein is κ-casein and the structured mammalian protein isβ-lactoglobulin.

Food Compositions Comprising a Fusion Protein

The fusion proteins and transgenic plants described herein may be usedto prepare food compositions. The fusion protein may be used directly toprepare the food composition (i.e., in the form of a fusion protein), orthe fusion protein may first be separated into its constituent proteins.For example, in some embodiments, a food composition may comprise either(i) a fusion protein, (ii) an unstructured milk protein, (iii) astructured mammalian, avian, or plant protein, or (iv) an unstructuredmilk protein and a structured mammalian, avian, or plant protein. Anillustrative method for preparing a food composition of the disclosureis provided in FIG. 11.

In some embodiments, the fusion proteins and transgenic plants describedherein may be used to prepare a food composition selected from cheeseand processed cheese products, yogurt and fermented dairy products,directly acidified counterparts of fermented dairy products, cottagecheese dressing, frozen dairy products, frozen desserts, desserts, bakedgoods, toppings, icings, fillings, low-fat spreads, dairy-based drymixes, soups, sauces, salad dressing, geriatric nutrition, creams andcreamers, analog dairy products, follow-up formula, baby formula, infantformula, milk, dairy beverages, acid dairy drinks, smoothies, milk tea,butter, margarine, butter alternatives, growing up milks, low-lactoseproducts and beverages, medical and clinical nutrition products,protein/nutrition bar applications, sports beverages, confections, meatproducts, analog meat products, meal replacement beverages, and weightmanagement food and beverages.

In some embodiments the fusion proteins and transgenic plants describedherein may be used to prepare a dairy product. In some embodiments, thedairy product is a fermented dairy product. An illustrative list offermented dairy products includes cultured buttermilk, sour cream,yogurt, skyr, leben, lassi, or kefir. In some embodiments the fusionproteins and transgenic plants described herein may be used to preparecheese products.

In some embodiments the fusion proteins and transgenic plants describedherein may be used to prepare a powder containing a milk protein. Insome embodiments, the fusion proteins and transgenic plants describedherein may be used to prepare a low-lactose product.

In some embodiments, a method for making a food composition comprises,expressing a recombinant fusion protein of the disclosure in a plant,extracting the recombinant fusion protein from the plant, optionallyseparating the milk protein from the structured mammalian or plantprotein, and creating a food composition using the fusion protein and/orthe milk protein.

The recombinant fusion proteins may be extracted from a plant usingstandard methods known in the art. For example, the fusion proteins maybe extracted using solvent or aqueous extraction. In some embodiments,the fusion proteins may be extracted using phenol extraction. Onceextracted, the fusion proteins may be maintained in a bufferedenvironment (e.g., Tris, MOPS, HEPES), in order to avoid sudden changesin the pH. The fusion proteins may also be maintained at a particulartemperature, such as 4° C. In some embodiments, one or more additivesmay be used to aid the extraction process (e.g., salts,protease/peptidase inhibitors, osmolytes, reducing agents, etc.)

In some embodiments, a method for making a food composition comprises,expressing a recombinant fusion protein of the disclosure in a plant,extracting one or both of the unstructured milk protein and thestructured mammalian or plant protein from the plant, and creating afood composition using the milk protein.

In some embodiments, the milk protein and the structured mammalian orplant protein are separated from one another in the plant cell, prior toextraction. In some embodiments, the milk protein is separated from thestructured mammalian or plant protein after extraction, for example bycontacting the fusion protein with an enzyme that cleaves the fusionprotein. The enzyme may be, for example, chymosin. In some embodiments,the fusion protein is cleaved using rennet.

All references, articles, publications, patents, patent publications,and patent applications cited herein are incorporated by reference intheir entireties for all purposes. However, mention of any reference,article, publication, patent, patent publication, and patent applicationcited herein is not, and should not be taken as an acknowledgment or anyform of suggestion that they constitute valid prior art or form part ofthe common general knowledge in any country in the world, or that theydisclose essential matter.

EXAMPLES

The following experiments demonstrate different recombinant fusionconstructs of milk proteins and structured proteins, as well as methodsof testing and producing the recombinant proteins, and food compositionsproduced from the extracted protein. While the examples below describeexpression in soybean, it will be understood by those skilled in the artthat the constructs and methods disclosed herein may be tailored forexpression in any organism.

Example 1: Construction of Expression Vectors for Plant Transformationfor Stable Expression of Recombinant Fusion Proteins Binary VectorDesign

While a number of vectors may be utilized for expression of the fusionproteins disclosed herein, the example constructs described below werebuilt in the binary pCAMBIA3300 (Creative Biogene, VET1372) vector,which was customized for soybean transformation and selection. In orderto modify the vector, pCAMBIA3300 was digested with HindIII and AseIallowing the release of the vector backbone (LB T-DNA repeat_KanR_pBR322ori_pBR322 bom_pVS1 oriV_pVs1 repA_pVS1 StaA_RB T-DNA repeat). The 6598bp vector backbone was gel extracted and a synthesized multiple cloningsite (MCS) was ligated via In-Fusion cloning (In-Fusion® HD CloningSystem CE, available on the world wide web at clontech.com) to allowmodular vector modifications. A cassette containing the Arabidopsisthaliana Csr1.2 gene for acetolactate synthase was added to the vectorbackbone to be used as a marker for herbicide selection of transgenicplants. In order to build this cassette, the regulatory sequences fromSolanum tuberosum ubiquitin/ribosomal fusion protein promoter (StUbi3prom; −1 to −922 bp) and terminator (StUbi3 term; 414 bp) (GenBankaccession no. L22576.1) were fused to the mutant (S653N) acetolactatesynthase gene (Csr1.2; GenBank accession no. X51514.1) (Sathasivan etal, 1990; Ding et al, 2006) to generate imazapyr-resistant traits insoybean plants. The selectable marker cassette was introduced into thedigested (EcoRI) modified vector backbone via In-Fusion cloning to formvector pAR15-00 (FIG. 2).

Recombinant DNA constructs were designed to express milk proteins(intrinsically unstructured and structured) in transgenic plants. Thecoding regions of the expression cassettes outlined below contain afusion of codon-optimized nucleic acid sequences encoding bovine milkproteins, or a functional fragment thereof. To enhance proteinexpression in soybean, the nucleic acid sequences encodingβ-lactoglobulin (GenBank accession no. X14712.1) κ-casein (GenBankaccession no. CAA25231), β-casein (GenBank accession no. M15132.1), andaS1-casein (GenBank accession no. X59836.1) were codon optimized usingGlycine max codon bias and synthesized (available on the world wide webat idtdna.com/CodonOpt). The signal sequences were removed (i.e., makingthe constructs “truncated”) and the new versions of the genes wererenamed as OLG1 (β-lactoglobulin version 1, SEQ ID NO: 9), OLG2(β-lactoglobulin version 2, SEQ ID NO: 11), OLG3 (β-lactoglobulinversion 3, SEQ ID NO: 12), OLG4 (β-lactoglobulin version 4, SEQ ID NO:13), OKC1-T (Optimized κ-casein Truncated version 1, SEQ ID NO: 3),paraOKC1-T (only the para-κ portion of OKC1-T, SEQ ID NO: 1), OBC-T2(Optimized β-casein Truncated version 2, SEQ ID NO: 5), and OaS1-T(Optimized αS1-casein Truncated version 1, SEQ ID NO: 7). As will beunderstood by those skilled in the art, any codon optimized nucleic acidsequences can present from 60% to 100% identity to the native version ofthe nucleic acid sequence.

All the expression cassettes described below and shown in FIG. 3-8contained codon-optimized nucleic acid sequences encoding bovine milkproteins, or a functional fragment thereof, a seed specific promoter, a5′UTR, a signal sequence (Sig) that directs foreign proteins to theprotein storage vacuoles, and a termination sequence. In some versionsof the constructs a linker (FM) such as chymosin cleavage site, wasplaced between the two proteins and/or a C-terminal KDEL sequence for ERretention was included. Expression cassettes were inserted in thepAR15-00 vector described above utilizing a KpnI restriction site withthe MCS (FIG. 2). Coding regions and regulatory sequences are indicatedas blocks (not to scale) in FIG. 3-8.

κ-casein-β-lactoglobulin Fusion with KDEL

Shown in FIG. 3 is an example expression cassette comprising κ-casein(OKC1-T, SEQ ID NO: 3) and β-lactoglobulin (OLG1, SEQ ID NO: 9). Theregulatory sequences that were used in order to produce the heterologousmilk proteins in soybean seeds include the promoter of thebeta-phaseolin storage protein gene (PvPhas prom; −1 to −1543; GenBankaccession no. J01263.1, SEQ ID NO: 18); the 5′UTR of the arc5-1 gene(arc5′UTR; −1 to −13; GenBank accession no. Z50202, SEQ ID NO: 20) (DeJaeger et al, 2002); the signal peptide of Lectin 1 gene 1 (sig10; +1 to+93; GenBank accession no. Glyma.02G012600, SEQ ID NO: 14) (Darnowski etal, 20020); and, the 3′UTR of the arc5-1 gene, (arc term 1197 bp;GenBank accession no. Z50202.1, SEQ ID NO: 21) (De Jaeger et al, 2002).A C-terminal KDEL (SEQ ID NO: 23) was also included for ER retention.

β-casein-β-lactoglobulin Fusion with Linker

Shown in FIG. 4 is an example expression cassette comprising β-casein(OBC-T2, SEQ ID NO: 5) and β-lactoglobulin (OLG1, SEQ ID NO: 9). Theregulatory sequences that were used in order to produce the heterologousmilk proteins in soybean seeds include the promoter of thebeta-phaseolin storage protein gene (PvPhas prom; −1 to −1543; GenBankaccession no. J01263.1, SEQ ID NO: 18); the 5′UTR of the arc5-1 gene(arc5′UTR; −1 to −13; GenBank accession no. Z50202, SEQ ID NO: 20) (DeJaeger et al, 2002); the signal peptide of Lectin 1 gene 1 (sig10; +1 to+93; accession no. Glyma.02G012600, SEQ ID NO: 14) (Darnowski et al,2002); and, the 3′UTR of the arc5-1 gene, (arc term 1197 bp; accessionno. Z50202.1, SEQ ID NO: 21) (De Jaeger, et al 2002). A linker (FM)comprising a chymosin cleavage site was inserted between the twoproteins.

αS1-casein-β-lactoglobulin Fusion with Linker

Shown in FIG. 5 is an example expression cassette comprising aS1-casein(OaS1-T, SEQ ID NO: 7) and β-lactoglobulin (OLG1, SEQ ID NO: 9). Theregulatory sequences that were used in order to produce the heterologousmilk proteins in soybean seeds include the promoter of thebeta-phaseolin storage protein gene (PvPhas prom; −1 to −1543; GenBankaccession no. J01263.1, SEQ ID NO: 18); the 5′UTR of the arc5-1 gene(arc5′UTR; −1 to −13; GenBank accession no. Z50202, SEQ ID NO: 20) (DeJaeger et al, 2002); the signal peptide of Lectin 1 gene 1 (sig10; +1 to+93; accession no. Glyma.02G012600, SEQ ID NO: 14) (Darnowski et al,2002); and, the 3′UTR of the arc5-1 gene, (arc term 1197 bp; GenBankaccession no. Z50202.1, SEQ ID NO: 21)(De Jaeger et al, 2002). A linker(FM) comprising a chymosin cleavage site was inserted between the twoproteins.

Para-κ-casein-β-lactoglobulin Fusion with Linker and KDEL

Shown in FIG. 6 is an example expression cassette comprisingpara-κ-casein (paraOKC1-T, SEQ ID NO: 1) and β-lactoglobulin (OLG1, SEQID NO: 9). The regulatory sequences that were used in order to producethe heterologous milk proteins in soybean seeds include the promoter ofthe beta-phaseolin storage protein gene (PvPhas prom; −1 to −1543;GenBank accession no. J01263.1, SEQ ID NO: 18); the 5′UTR of the arc5-1gene (arc5′UTR; −1 to −13; GenBank accession no. Z50202, SEQ ID NO: 20)(De Jaeger et al, 2002); the signal peptide of Lectin 1 gene 1 (sig10;+1 to +93; GenBank accession no. Glyma.02G012600, SEQ ID NO: 14)(Darnowski et al, 2002); and, the 3′UTR of the arc5-1 gene, (arc term1197 bp; GenBank accession no. Z50202.1, SEQ ID NO: 21) (De Jaeger et al2002). A linker (FM) comprising a chymosin cleavage site was insertedbetween the two proteins and a C-terminal KDEL (SEQ ID NO: 23) was alsoincluded for ER retention.

Para-κ-casein-β-lactoglobulin Fusion with Linker

Shown in FIG. 7 is an example expression cassette comprisingpara-κ-casein (paraOKC1-T, SEQ ID NO: 1) and β-lactoglobulin (OLG1, SEQID NO: 9). The regulatory sequences that were used in order to producethe heterologous milk proteins in soybean seeds include the promoter ofthe beta-phaseolin storage protein gene (PvPhas prom; −1 to −1543;GenBank accession no. J01263.1, SEQ ID NO: 18); the 5′UTR of the arc5-1gene (arc5′UTR; −1 to −13; GenBank accession no. Z50202, SEQ ID NO: 20)(De Jaeger et al, 2002); the signal peptide of Lectin 1 gene 1 (sig10;+1 to +93; GenBank accession no. Glyma.02G012600, SEQ ID NO: 14)(Darnowski et al, 2002); and, the 3′UTR of the arc5-1 gene, (arc term1197 bp; GenBank accession no. Z50202.1, SEQ ID NO: 21) (De Jaeger etal, 2002). A linker (FM) comprising a chymosin cleavage site wasinserted between the two proteins.

Fusion Protein with Seed2 Promoter, Sig2 and Nopaline SynthaseTerminator

Shown in FIG. 8 is an example expression cassette comprising κ-casein(OKC1-T, SEQ ID NO: 3) and β-lactoglobulin (OLG1, SEQ ID NO: 9). Theregulatory sequences that were used in order to produce the heterologousmilk proteins in soybean seeds include the promoter and signal peptideof glycinin 1 (GmSeed2 (SEQ ID NO: 19): sig2 (SEQ ID NO: 16)) followedby the ER retention signal (KDEL) and the Nopaline synthase terminationsequence (nos term, SEQ ID NO: 22).

Example 2: Identification of Transgenic Events, Recombinant ProteinExtraction and Detection

To quantify recombinant protein expression levels, DNA constructs suchas those shown in FIG. 3-8 were transformed into soybean usingtransformation protocols well known in the art, for example, bybombardment or Agrobacterium. Total soybean genomic DNA was isolatedfrom the first trifoliate leaves of transgenic events using the PureGenetissue DNA isolation kit (product #158667: QIAGEN, Valencia, Calif.,USA). Trifoliates were frozen in liquid nitrogen and pulverized. Cellswere lysed using the PureGene Cell Lysis Buffer, proteins wereprecipitated using the PureGene Protein Precipitation Buffer, and DNAwas precipitated from the resulting supernatant using ethanol. The DNApellets were washed with 70% ethanol and resuspended in water.

Genomic DNA was quantified by the Quant-iT PicoGreen (product #P7589:ThermoFisher Scientific, Waltham, Mass., USA) assay as described bymanufacturer, and 150 ng of DNA was digested overnight with EcoRI,HindIII, NcoI, and/or KpnI, 30 ng of which was used for a BioRad ddPCRreaction, including labelled FAM or HEX probes for the transgene andLectin1 endogenous gene respectively. Transgene copy number (CNV) wascalculated by comparing the measured transgene concentration to thereference gene concentration. A CNV of greater than or equal to one wasdeemed acceptable.

Preparation of Total Soluble Protein Samples

Total soluble soybean protein fractions were prepared from the seeds oftransgenic events by bead beating seeds (seeds collected about 90 daysafter germination) at 15000 rpm for 1 min. The resulting powder wasresuspended in 50 mM Carbonate-Bicarbonate pH 10.8, 1 mM DTT, 1×HALTProtease Inhibitor Cocktail (Product #78438 ThermoFisher Scientific).The resuspended powder was incubated at 4° C. for 15 minutes and thenthe supernatant collected after centrifuging twice at 4000 g, 20 min, 4°C. Protein concentration was measured using a modified Bradford assay(Thermo Scientific Pierce 660 nm assay; Product #22660 ThermoFisherScientific) using a bovine serum albumin (BSA) standard curve.

Recombinant Protein Quantification via Western Blot Densitometry

SDS-PAGE was performed according to manufacturer's instructions (Product#5678105BioRad, Hercules, Calif., USA) under denaturing and reducingconditions. 5 ug of total protein extracts were loaded per lane. Forimmunoblotting proteins separated by SDS-PAGE were transferred to a PVDFmembrane using Trans-Blot® Turbo™ Midi PVDF Transfer Packs (Product#1704157 BioRad) according to manufacturer's guidelines. Membranes wereblocked with 3% BSA in phosphate buffered saline with 0.5% Tween-20,reacted with antigen specific antibody and subsequently reacted withfluorescent goat anti rabbit IgG (Product #60871 BioRad, CA). Membraneswere scanned according to manufacturer's instructions using the ChemiDocMP Imaging System (BioRad, CA) and analyzed using ImageLab Version 6.0.1Standard Edition (BioRad Laboratories, Inc.). Recombinant protein fromthe seeds of transgenic events was quantified by densitometry fromcommercial reference protein spike-in standards.

Shown in FIGS. 9A, 9B, 9C, and 9D are Western Blots of protein extractedfrom transgenic soybeans expressing the κ-casein-β-lactoglobulinexpression cassette shown in FIG. 3. FIG. 9A shows the fusion proteindetected using a primary antibody raised against κ-casein. The firstlane is a molecular weight marker. Lanes two (DCI 9.1) and three (DCI9.2) represent individual seeds from a single transgenic line. Lane four(DCI 3.1) represents a seed from a separate transgenic line. Lane fiveis protein extracted from wild-type soybean plants, and lanes six-eightare protein extracted from wild-type soybean plants spiked with 0.05%commercial κ-casein (lane 6), 0.5% commercial κ-casein (lane 7), and1.5% commercial κ-casein (lane 8). The κ-casein commercial protein isdetected at an apparent molecular weight (MW) of ˜26 kDa (theoretical:19 kDa—arrow). The fusion protein is detected at an apparent MW of ˜40kDa (theoretical: 38 kDa—arrowhead).

FIG. 9B shows the fusion protein detected using a primary antibodyraised against β-lactoglobulin. The first lane is a molecular weightmarker. Lanes two (DCI 9.1) and three (DCI 9.2) represent individualseeds from a single transgenic line. Lane four (DCI 3.1) represents aseed from a separate transgenic line. Lane five is protein extractedfrom wild-type soybean plants, and lanes six-eight are protein extractedfrom wild-type soybean plants spiked with 0.05% commercialβ-lactoglobulin (lane 6), 1% commercial β-lactoglobulin (lane 7), and 2%commercial β-lactoglobulin (lane 8). The β-lactoglobulin commercialprotein is detected at an apparent MW of ˜18 kDa (theoretical: 18kDa—arrow). The fusion protein is detected at an apparent MW of ˜40 kDa(theoretical: 38 kDa—arrowhead). FIGS. 9C and 9D show the protein gelsas control for equal lane loading (image is taken at the end of the SDSrun) for FIGS. 9A and 9B, respectively.

Other combinations of structured and unstructured proteins were testedand evaluated for the percentage of recombinant protein. Cassetteshaving the same promoter (Seed2-sig), signal peptide (EUT:Rb7T), and insome instances a different terminator, were built with eitherα-S1-casein, β-casein, κ-casein, or the fusion of β-lactoglobulin withκ-casein (kCN-LG) (See FIGS. 3 and 8). As shown below in Table 3, noneof the cassettes encoding α-S1-casein, β-casein, or κ-casein were ableto produce expression of the protein at a level that exceeded 1% totalsoluble protein. However, when κ-casein was fused with β-lactoglobulin,κ-casein was expressed at a level that was greater than 1% total solubleprotein.

TABLE 3 Expression levels of unstructured proteins Number of events¹accumulating the Total recombinant protein at the events¹ concentration:analyzed 0-1% TSP Above 1% TSP Unstructured κ-Casein 89 89 0 B-Casein 1212 0 αS1-Casein 6 6 0 Fusion kCN-LG 23 12 11 ¹As used in Table 3, theeach “event” refers to an independent transgenic line.

As will be readily understood by those of skill in the art, T-DNAinsertion into the plant genome is a random process and each T-DNA landsat an unpredictable genomic position. Hence, each of the 23 eventsgenerated in Table 3 for the fusion protein have different genomicinsertion loci. The genomic context greatly influences the expressionlevels of a gene, and each loci will be either favorable or unfavorablefor the expression of the recombinant genes. The variability observed atthe protein level is a reflection of that random insertion process, andexplains why 12 out of 23 events present expression levels below 1%.

Example 3: Food Compositions

The transgenic plants expressing the recombinant fusion proteinsdescribed herein can produce milk proteins for the purpose of foodindustrial, non-food industrial, pharmaceutical, and commercial usesdescribed in this disclosure. An illustrative method for making a foodcomposition is provided in FIG. 11.

A fusion protein comprising an unstructured milk protein (para-κ-casein)and a structured mammalian protein (β-lactoglobulin) is expressed in atransgenic soybean plant. The fusion protein comprises a chymosincleavage site between the para-κ-casein and the β-lactoglobulin.

The fusion protein is extracted from the plant. The fusion protein isthen treated with chymosin, to separate the para-κ-casein from theβ-lactoglobulin. The para-κ-casein is isolated and/or purified and usedto make a food composition (e.g., cheese).

Numbered Embodiments

Notwithstanding the appended claims, the following numbered embodimentsalso form part of the instant disclosure.

1. A stably transformed plant comprising in its genome: a recombinantDNA construct encoding a fusion protein, the fusion protein comprising:(i) an unstructured milk protein, and (ii) a structured animal protein;wherein the fusion protein is stably expressed in the plant in an amountof 1% or higher per total protein weight of soluble protein extractablefrom the plant.

2. The stably transformed plant of embodiment 1, wherein the fusionprotein comprises, from N-terminus to C-terminus, the unstructured milkprotein and the animal protein.

3. The stably transformed plant of any one of embodiments 1-2, whereinthe unstructured milk protein is α-S1 casein, α-S2 casein, β-casein, orκ-casein.

4. The stably transformed plant of embodiment 1, wherein theunstructured milk protein is κ-casein and comprises the sequence of SEQID NO: 4, or a sequence at least 90% identical thereto.

5. The stably transformed plant of embodiment 1, wherein theunstructured milk protein is para-κ-casein and comprises the sequence ofSEQ ID NO: 2, or a sequence at least 90% identical thereto.

6. The stably transformed plant of embodiment 1, wherein theunstructured milk protein is β-casein and comprises the sequence of SEQID NO: 6, or a sequence at least 90% identical thereto.

7. The stably transformed plant of embodiment 1, wherein theunstructured milk protein is α-S1 casein and comprises the sequence SEQID NO: 8, or a sequence at least 90% identical thereto.

8. The stably transformed plant of embodiment 1, wherein theunstructured milk protein is α-S2 casein and comprises the sequence SEQID NO: 84, or a sequence at least 90% identical thereto.

9. The stably transformed plant of any one of embodiments 1-8, whereinthe structured animal protein is a structured mammalian protein.

10. The stably transformed plant of embodiment 9, wherein the structuredmammalian protein is β-lactoglobulin, α-lactalbumin, albumin, lysozyme,lactoferrin, lactoperoxidase, hemoglobin, collagen, or animmunoglobulin.

11. The stably transformed plant of embodiment 9, wherein the structuredmammalian protein is β-lactoglobulin and comprises the sequence of SEQID NO: 10, or a sequence at least 90% identical thereto.

12. The stably transformed plant of any one of embodiments 1-8, whereinthe structured animal protein is a structured avian protein.

13. The stably transformed plant embodiment 12, wherein the structuredavian protein is ovalbumin, ovotransferrin, lysozyme or ovoglobulin.

14. The stably transformed plant of embodiment 9, wherein the milkprotein is κ-casein and the structured mammalian protein isβ-lactoglobulin.

15. The stably transformed plant of embodiment 9, wherein the milkprotein is para-κ-casein and the structured mammalian protein isβ-lactoglobulin.

16. The stably transformed plant of embodiment 9, wherein the milkprotein is β-casein and the structured mammalian protein isβ-lactoglobulin.

17. The stably transformed plant of embodiment 9, wherein the milkprotein is α-S1 casein or α-S2 casein and the structured mammalianprotein is β-lactoglobulin.

18. The stably transformed plant of any one of embodiments 1-17, whereinthe plant is a dicot.

19. The stably transformed plant of embodiment 18, wherein the dicot isArabidopsis, tobacco, tomato, potato, sweet potato, cassava, alfalfa,lima bean, pea, chick pea, soybean, carrot, strawberry, lettuce, oak,maple, walnut, rose, mint, squash, daisy, Quinoa, buckwheat, mung bean,cow pea, lentil, lupin, peanut, fava bean, French beans (i.e., commonbeans), mustard, or cactus.

20. The stably transformed plant of any one of embodiments 1-19, whereinthe plant is soybean.

21. The stably transformed plant of any one of embodiments 1-20, whereinthe recombinant DNA construct is codon-optimized for expression in theplant.

22. The stably transformed plant of any one of embodiments 1-21, whereinthe fusion protein comprises a protease cleavage site.

23. The stably transformed plant of embodiment 22, wherein the proteasecleavage site is a chymosin cleavage site.

24. The stably transformed plant of any one of embodiments 1-23, whereinthe fusion protein is expressed at a level at least 2-fold higher thanan unstructured milk protein expressed individually in a plant.

25. The stably transformed plant of any one of embodiments 1-24, whereinthe fusion protein accumulates in the plant at least 2-fold higher thanan unstructured milk protein expressed without the structured animalprotein.

26. A recombinant fusion protein comprising: (i) an unstructured milkprotein, and (ii) a structured animal protein.

27. The recombinant fusion protein of embodiment 26, wherein the fusionprotein is expressed in a plant.

28. The recombinant fusion protein of embodiment 26 or 27, wherein theunstructured milk protein is α-S1 casein, α-S2 casein, β-casein, orκ-casein.

29. The recombinant fusion protein of embodiment 28, wherein the milkprotein is κ-casein and comprises the sequence of SEQ ID NO: 4, or asequence at least 90% identical thereto.

30. The recombinant fusion protein of embodiment 28, wherein the milkprotein is para-κ-casein and comprises the sequence of SEQ ID NO: 2, ora sequence at least 90% identical thereto.

31. The recombinant fusion protein of embodiment 28, wherein the milkprotein is β-casein and comprises the sequence of SEQ ID NO: 6, or asequence at least 90% identical thereto.

32. The recombinant fusion protein of embodiment 28, wherein the milkprotein is α-S1 casein and comprises the sequence SEQ ID NO: 8, or asequence at least 90% identical thereto.

33. The recombinant fusion protein of embodiment 28, wherein the milkprotein is α-S2 casein and comprises the sequence SEQ ID NO: 84, or asequence at least 90% identical thereto.

34. The recombinant fusion protein of any one of embodiments 26-33,wherein the structured animal protein is a structured mammalian protein.

35. The recombinant fusion protein of embodiment 34, wherein thestructured mammalian protein is β-lactoglobulin, α-lactalbumin, albumin,lysozyme, lactoferrin, lactoperoxidase, hemoglobin, collagen, or animmunoglobulin.

36. The recombinant fusion protein of embodiment 34, wherein thestructured mammalian protein is β-lactoglobulin and comprises thesequence of SEQ ID NO: 10, or a sequence at least 90% identical thereto.

37. The recombinant fusion protein of any one of embodiments 26-33,wherein the structured animal protein is a structured avian protein.

38. The recombinant fusion protein of embodiment 37, wherein thestructured avian protein is ovalbumin, ovotransferrin, lysozyme orovoglobulin.

39. The recombinant fusion protein embodiment 34, wherein the milkprotein is κ-casein and the structured mammalian protein isβ-lactoglobulin.

40. The recombinant fusion protein of embodiment 34, wherein the milkprotein is para-κ-casein and the structured mammalian protein isβ-lactoglobulin.

41. The recombinant fusion protein of embodiment 34, wherein the milkprotein is β-casein and the structured mammalian protein isβ-lactoglobulin.

42. The recombinant fusion protein of embodiment 34, wherein the milkprotein is α-S1 casein or α-S2 casein and the structured mammalianprotein is β-lactoglobulin.

43. The recombinant fusion protein of embodiment 34, wherein the fusionprotein comprises a protease cleavage site.

44. The recombinant fusion protein of embodiment 34, wherein theprotease cleavage site is a chymosin cleavage site.

45. A nucleic acid encoding the recombinant fusion protein of any one ofembodiments 26 to 44.

46. The nucleic acid of embodiment 45, wherein the nucleic acid is codonoptimized for expression in a plant species.

47. The nucleic of embodiment 45 or 46, wherein the nucleic acid iscodon optimized for expression in soybean.

48. A vector comprising a nucleic acid encoding a recombinant fusionprotein, wherein the recombinant fusion protein comprises: (i) anunstructured milk protein, and (ii) a structured animal protein.

49. The vector of embodiment 48, wherein the vector is a plasmid.

50. The vector of embodiment 49, wherein the vector is an AgrobacteriumTi plasmid.

51. The vector of any one of embodiments 48-50, wherein the nucleic acidcomprises, in order from 5′ to 3′: a promoter; a 5′ untranslated region;a sequence encoding the fusion protein; and a terminator.

52. The vector of embodiment 51, wherein the promoter is a seed-specificpromoter.

53. The vector of embodiment 52, wherein the seed-specific promoter isselected from the group consisting of PvPhas, BnNap, AtOle1, GmSeed2,GmSeed3, GmSeed5, GmSeed6, GmSeed7, GmSeed8, GmSeed10, GmSeed11,GmSeed12, pBCON, GmCEP1-L, GmTHIC, GmBg7S1, GmGRD, GmOLEA, GmOLER,Gm2S-1, and GmBBld-II.

54. The vector of embodiment 53, wherein the seed-specific promoter isPvPhas and comprises the sequence of SEQ ID NO: 18, or a sequence atleast 90% identical thereto.

55. The vector of embodiment 53, wherein the seed-specific promoter isGmSeed2 and comprises the sequence of SEQ ID NO: 19, or a sequence atleast 90% identical thereto.

56. The vector of any one of embodiments 51-55, wherein the 5′untranslated region is selected from the group consisting of Arc5′UTRand glnBlUTR.

57. The vector of embodiment 56, wherein the 5′ untranslated region isArc5′UTR and comprises the sequence of SEQ ID NO: 20, or a sequence atleast 90% identical thereto.

58. The vector of any one of embodiments 51-57, wherein the expressioncassette comprises a 3′ untranslated region.

59. The vector of embodiment 58, wherein the 3′ untranslated region isArc5-1 and comprises SEQ ID NO: 21, or a sequence at least 90% identicalthereto.

60. The vector of any one of embodiments 51-59, wherein the terminatorsequence is a terminator isolated or derived from a gene encodingNopaline synthase, Arc5-1, an Extensin, Rb7 matrix attachment region, aHeat shock protein, Ubiquitin 10, Ubiquitin 3, and M6 matrix attachmentregion.

61. The vector of embodiment 60, wherein the terminator sequence isisolated or derived from a Nopaline synthase gene and comprises thesequence of SEQ ID NO: 22, or a sequence at least 90% identical thereto.

62. A plant comprising the recombinant fusion protein of any one ofembodiments 26-44 or the nucleic acid of any one of embodiments 45-47.

63. A method for stably expressing a recombinant fusion protein in aplant, the method comprising: a) transforming a plant with a planttransformation vector comprising an expression cassette comprising: asequence encoding a fusion protein, wherein the fusion protein comprisesan unstructured milk protein, and a structured animal protein; and b)growing the transformed plant under conditions wherein the recombinantfusion protein is expressed in an amount of 1% or higher per totalprotein weight of soluble protein extractable from the plant.

64. The method of embodiment 63, wherein the unstructured milk proteinis κ-casein.

65. The method of embodiment 63 or 64, wherein the structured animalprotein is β-lactoglobulin.

66. A food composition comprising the recombinant fusion protein of anyone of embodiments 26-44.

67. A method for making a food composition, the method comprising:expressing the recombinant fusion protein of any one of embodiments26-44 in a plant; extracting the recombinant fusion protein from theplant; optionally, separating the milk protein from the structuredanimal protein or the structured plant protein; and creating a foodcomposition using the milk protein or the fusion protein.

68. The method of embodiment 67, wherein the plant stably expresses therecombinant fusion protein.

69. The method of embodiment 68, wherein the plant expresses therecombinant fusion protein in an amount of 1% or higher per totalprotein weight of soluble protein extractable from the plant.

70. The method of any one of embodiments 67-69, wherein the plant issoybean.

71. The method of any one of embodiments 67-70, wherein the foodcomposition comprises the structured animal or plant protein.

72. The method of any one of embodiments 67-71, wherein the milk proteinand the structured animal or plant protein are separated from oneanother in the plant cell, prior to extraction.

73. The method of any one of embodiments 67-71, wherein the milk proteinis separated from the structured animal or plant protein afterextraction, by contacting the fusion protein with an enzyme that cleavesthe fusion protein.

74. A food composition produced using the method of any one ofembodiments 67-73.

75. A plant-expressed recombinant fusion protein, comprising: κ-casein;and β-lactoglobulin.

76. The plant-expressed recombinant fusion protein of embodiment 75,wherein the fusion protein comprises, in order from N-terminus toC-terminus, the κ-casein and the β-lactoglobulin.

77. The plant-expressed recombinant fusion protein of embodiment 75 or76, wherein the fusion protein comprises a protease cleavage site.

78. The plant-expressed recombinant fusion protein of embodiment 77,wherein the protease cleavage site is a chymosin cleavage site.

79. The plant-expressed recombinant fusion protein of any one ofembodiments 75-78, wherein the fusion protein comprises a signalpeptide.

80. The plant-expressed recombinant fusion protein of embodiment 79,wherein the signal peptide is located at the N-terminus of the fusionprotein.

81. The plant-expressed recombinant fusion protein of any one ofembodiments 75-80, wherein the fusion protein is encoded by a nucleicacid that is codon optimized for expression in a plant.

82. The plant-expressed recombinant fusion protein of any one ofembodiments 75-81, wherein the fusion protein is expressed in a soybean.

83. The plant-expressed recombinant fusion protein of any one ofembodiments 75-81, wherein the fusion protein has a molecular weight of30 kDa to 50 kDa.

84. The plant-expressed recombinant fusion protein of any one ofembodiments 75-83, wherein the fusion protein is expressed in a plant inan amount of 1% or higher per total protein weight of soluble proteinextractable from the plant.

85. The plant-expressed recombinant fusion protein of any one ofembodiments 75-84, wherein the fusion protein is expressed in the plantat a level at least 2-fold higher than κ-casein expressed individuallyin a plant.

86. The plant-expressed recombinant fusion protein of any one ofembodiments 75-84, wherein the fusion protein accumulates in the plantat least 2-fold higher than κ-casein expressed without β-lactoglobulin.

87. A stably transformed plant, comprising in its genome: a recombinantDNA construct encoding a fusion protein, the fusion protein comprising:κ-casein; and β-lactoglobulin; wherein the fusion protein is stablyexpressed in the plant in an amount of 1% or higher per total proteinweight of soluble protein extractable from the plant.

88. The stably transformed plant of embodiment 87, wherein the fusionprotein comprises, in order from N-terminus to C-terminus, the κ-caseinand the β-lactoglobulin.

89. The stably transformed plant of embodiment 87 or 88, wherein thefusion protein comprises a protease cleavage site.

90. The stably transformed plant of embodiment 89, wherein the proteasecleavage site is a chymosin cleavage site.

91. The stably transformed plant of any one of embodiments 87-90,wherein the fusion protein comprises a signal peptide.

92. The stably transformed plant of embodiment 91, wherein the signalpeptide is located at the N-terminus of the fusion protein.

93. The stably transformed plant of any one of embodiments 87-92,wherein the plant is soybean.

94. The stably transformed plant of any one of embodiments 87-93,wherein the recombinant DNA construct comprises codon-optimized nucleicacids for expression in the plant.

95. The stably transformed plant of any one of embodiments 87-94,wherein the fusion protein has a molecular weight of 30 kDa to 50 kDa.

96. The stably transformed plant of any one of embodiments 87-95,wherein the fusion protein is expressed at a level at least 2-foldhigher than κ-casein expressed individually in a plant.

97. The stably transformed plant of any one of embodiments 87-96,wherein the fusion protein accumulates in the plant at least 2-foldhigher than κ-casein expressed without β-lactoglobulin.

98. A plant-expressed recombinant fusion protein comprising: a caseinprotein and β-lactoglobulin.

99. The plant-expressed recombinant fusion protein of embodiment 98,wherein the casein protein is α-S1 casein, α-S2 casein, β-casein, orκ-casein.

100. A stably transformed plant, comprising in its genome: a recombinantDNA construct encoding a fusion protein, the fusion protein comprising:a casein protein and β-lactoglobulin; wherein the fusion protein isstably expressed in the plant in an amount of 1% or higher per totalprotein weight of soluble protein extractable from the plant.

101. The stably transformed plant of embodiment 100, wherein the caseinprotein is α-S1 casein, α-S2 casein, β-casein, or κ-casein.

What is claimed is:
 1. A recombinant fusion protein, comprising: a)casein; and b) β-lactoglobulin.
 2. The recombinant fusion protein ofclaim 1, further comprising a protease cleavage site.
 3. The recombinantfusion protein of claim 1, further comprising a chymosin cleavage site.4. The recombinant fusion protein of claim 1, wherein the casein isbovine.
 5. The recombinant fusion protein of claim 1, wherein theβ-lactoglobulin is bovine.
 6. The recombinant fusion protein of claim 1,wherein the casein and β-lactoglobulin are bovine.
 7. A nucleic acidmolecule encoding the recombinant fusion protein of claim
 1. 8. Thenucleic acid molecule of claim 7, wherein the nucleic acid sequence iscodon optimized for expression in a plant.
 9. The nucleic acid moleculeof claim 8, wherein the plant is a soybean plant.
 10. An expressionvector comprising the nucleic acid molecule of claim
 7. 11. A host cellcomprising the expression vector of claim
 10. 12. The host cell of claim11, wherein the host cell is selected from the group consisting of plantcells, bacterial cells, fungal cells, and mammalian cells.
 13. The hostcell of claim 11, wherein the host cell is a plant cell.
 14. A plantstably transformed with the nucleic acid molecule of claim
 7. 15. Theplant of claim 14, wherein the plant is a monocot selected from thegroup consisting of turf grass, maize, rice, oat, wheat, barley,sorghum, orchid, iris, lily, onion, palm, and duckweed.
 16. The plant ofclaim 14, wherein the plant is a dicot selected from the groupconsisting of Arabidopsis, tobacco, tomato, potato, sweet potato,cassava, alfalfa, lima bean, pea, chick pea, soybean, carrot,strawberry, lettuce, oak, maple, walnut, rose, mint squash, daisy,quinoa, buckwheat, mung bean, cow pea, lentil, lupin, peanut, fava bean,French beans, mustard, and cactus.
 17. The plant of claim 14, whereinthe plant is a soybean plant.
 18. A food composition, comprising: afusion protein comprising casein and β-lactoglobulin.
 19. The foodcomposition of claim 18, wherein the food composition is a solid. 20.The food composition of claim 18, wherein the food composition is aliquid.
 21. The food composition of claim 18, wherein the foodcomposition is a powder.
 22. The food composition of claim 18, whereinthe food composition is selected from the group consisting of: cheese,processed cheese product, yogurt, fermented dairy product, directlyacidified counterpart of fermented dairy product, cottage cheese,dressing, frozen dairy product, frozen dessert, dessert, baked good,topping, icing, filling, low-fat spread, dairy-based dry mix, soup,sauce, salad dressing, geriatric nutrition, cream, creamer, analog dairyproduct, follow-up formula, baby formula, infant formula, milk, dairybeverage, acid dairy drink, smoothie, milk tea, butter, margarine,butter alternative, growing up milk, low-lactose product, low-lactosebeverage, medical and clinical nutrition product, protein bar, nutritionbar, sport beverage, confection, meat product, analog meat product, mealreplacement beverage, weight management food and beverage, dairyproduct, cultured buttermilk, sour cream, skyr, leben, lassi, kefir,powder containing a milk protein, and low-lactose product.
 23. The foodcomposition of claim 18, wherein the food composition is a dairyproduct.
 24. The food composition of claim 18, wherein the foodcomposition is an analog dairy product.
 25. The food composition ofclaim 18, wherein the food composition is a low lactose product.
 26. Thefood composition of claim 18, wherein the food composition is a milk.27. The food composition of claim 18, wherein the food composition is acheese.
 28. The food composition of claim 18, wherein the foodcomposition is fermented.